{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T09:26:09Z","timestamp":1787131569418,"version":"build-2736575974"},"reference-count":165,"publisher":"Springer Science and Business Media LLC","license":[{"start":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T00:00:00Z","timestamp":1787097600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T00:00:00Z","timestamp":1787097600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Biotechnol"],"DOI":"10.1007\/s12033-026-01604-y","type":"journal-article","created":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T08:36:31Z","timestamp":1787128591000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement"],"prefix":"10.1007","author":[{"given":"Saikat","family":"Sena","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2081-3485","authenticated-orcid":false,"given":"Vijay","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,19]]},"reference":[{"key":"1604_CR1","unstructured":"The Human Genome Project. Retrieved from https:\/\/www.genome.gov\/human-genome-project (accessed June 30, 2026)."},{"key":"1604_CR2","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/j.pbi.2019.12.005","volume":"54","author":"MF Danilevicz","year":"2020","unstructured":"Danilevicz, M. F., Tay Fernandez, C. G., Marsh, J. I., Bayer, P. E., & Edwards, D. (2020). Plant pangenomics: Approaches, applications and advancements. Current Opinion in Plant Biology, 54, 18\u201325. https:\/\/doi.org\/10.1016\/j.pbi.2019.12.005","journal-title":"Current Opinion in Plant Biology"},{"key":"1604_CR3","doi-asserted-by":"publisher","first-page":"796","DOI":"10.1038\/35048692","volume":"408","author":"TAG Initiative","year":"2000","unstructured":"Initiative, T. A. G. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796\u2013815. https:\/\/doi.org\/10.1038\/35048692","journal-title":"Nature"},{"key":"1604_CR4","doi-asserted-by":"publisher","first-page":"793","DOI":"10.1038\/nature03895","volume":"436","author":"International Rice Genome Sequencing Project","year":"2005","unstructured":"International Rice Genome Sequencing Project. (2005). The map-based sequence of the rice genome. Nature, 436, 793\u2013800. https:\/\/doi.org\/10.1038\/nature03895","journal-title":"Nature"},{"key":"1604_CR5","doi-asserted-by":"publisher","first-page":"1571","DOI":"10.1038\/s41477-021-01031-8","volume":"7","author":"RA Marks","year":"2021","unstructured":"Marks, R. A., Hotaling, S., Frandsen, P. B., & VanBuren, R. (2021). Representation and participation across 20 years of plant genome sequencing. Nature Plants, 7, 1571\u20131578. https:\/\/doi.org\/10.1038\/s41477-021-01031-8","journal-title":"Nature Plants"},{"key":"1604_CR6","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1016\/j.tplants.2021.10.006","volume":"27","author":"Y Sun","year":"2022","unstructured":"Sun, Y., Shang, L., Zhu, Q.-H., Fan, L., & Guo, L. (2022). Twenty years of plant genome sequencing: Achievements and challenges. Trends in Plant Science, 27, 391\u2013401. https:\/\/doi.org\/10.1016\/j.tplants.2021.10.006","journal-title":"Trends in Plant Science"},{"key":"1604_CR7","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1016\/j.molp.2022.12.009","volume":"16","author":"J Shi","year":"2023","unstructured":"Shi, J., Tian, Z., Lai, J., & Huang, X. (2023). Plant pan-genomics and its applications. Molecular Plant, 16, 168\u2013186. https:\/\/doi.org\/10.1016\/j.molp.2022.12.009","journal-title":"Molecular Plant"},{"key":"1604_CR8","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1038\/s41477-018-0136-7","volume":"4","author":"F Cheng","year":"2018","unstructured":"Cheng, F., Wu, J., Cai, X., Liang, J., Freeling, M., & Wang, X. (2018). Gene retention, fractionation and subgenome differences in polyploid plants. Nature Plants, 4, 258\u2013268. https:\/\/doi.org\/10.1038\/s41477-018-0136-7","journal-title":"Nature Plants"},{"key":"1604_CR9","doi-asserted-by":"publisher","DOI":"10.3390\/genes9020088","volume":"9","author":"J Pellicer","year":"2018","unstructured":"Pellicer, J., Hidalgo, O., Dodsworth, S., & Leitch, I. J. (2018). Genome size diversity and its impact on the evolution of land plants. Genes, 9, Article 88. https:\/\/doi.org\/10.3390\/genes9020088","journal-title":"Genes"},{"key":"1604_CR10","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1016\/j.molp.2019.11.009","volume":"13","author":"H Liu","year":"2020","unstructured":"Liu, H., Shi, J., Cai, Z., Huang, Y., Lv, M., Du, H., Gao, Q., Zuo, Y., Dong, Z., Huang, W., Qin, R., Liang, C., Lai, J., & Jin, W. (2020). Evolution and domestication footprints uncovered from the genomes of Coix. Molecular Plant, 13, 295\u2013308. https:\/\/doi.org\/10.1016\/j.molp.2019.11.009","journal-title":"Molecular Plant"},{"key":"1604_CR11","doi-asserted-by":"publisher","first-page":"1757","DOI":"10.1016\/j.molp.2021.06.018","volume":"14","author":"J-M Song","year":"2021","unstructured":"Song, J.-M., Xie, W.-Z., Wang, S., Guo, Y.-X., Koo, D.-H., Kudrna, D., Gong, C., Huang, Y., Feng, J.-W., Zhang, W., Zhou, Y., Zuccolo, A., Long, E., Lee, S., Talag, J., Zhou, R., Zhu, X.-T., Yuan, D., Udall, J., \u2026 Chen, L.-L. (2021). Two gap-free reference genomes and a global view of the centromere architecture in rice. Molecular Plant, 14, 1757\u20131767. https:\/\/doi.org\/10.1016\/j.molp.2021.06.018","journal-title":"Molecular Plant"},{"key":"1604_CR12","doi-asserted-by":"publisher","DOI":"10.1126\/science.abi7489","volume":"374","author":"M Naish","year":"2021","unstructured":"Naish, M., Alonge, M., Wlodzimierz, P., Tock, A. J., Abramson, B. W., Schm\u00fccker, A., Mand\u00e1kov\u00e1, T., Jamge, B., Lambing, C., Kuo, P., Yelina, N., Hartwick, N., Colt, K., Smith, L. M., Ton, J., Kakutani, T., Martienssen, R. A., Schneeberger, K., Lysak, M. A., \u2026 Henderson, I. R. (2021). The genetic and epigenetic landscape of the Arabidopsis centromeres. Science, 374, Article eabi7489. https:\/\/doi.org\/10.1126\/science.abi7489","journal-title":"Science"},{"key":"1604_CR13","doi-asserted-by":"publisher","DOI":"10.1016\/j.copbio.2022.102886","volume":"79","author":"N Gladman","year":"2023","unstructured":"Gladman, N., Goodwin, S., Chougule, K., McCombie, W. R., & Ware, D. (2023). Era of gapless plant genomes: Innovations in sequencing and mapping technologies revolutionize genomics and breeding. Current Opinion in Biotechnology, 79, Article 102886. https:\/\/doi.org\/10.1016\/j.copbio.2022.102886","journal-title":"Current Opinion in Biotechnology"},{"key":"1604_CR14","doi-asserted-by":"publisher","first-page":"1221","DOI":"10.1038\/s41588-023-01419-6","volume":"55","author":"J Chen","year":"2023","unstructured":"Chen, J., Wang, Z., Tan, K., Huang, W., Shi, J., Li, T., Hu, J., Wang, K., Wang, C., Xin, B., Zhao, H., Song, W., Hufford, M. B., Schnable, J. C., Jin, W., & Lai, J. (2023). A complete telomere-to-telomere assembly of the maize genome. Nature Genetics, 55, 1221\u20131231. https:\/\/doi.org\/10.1038\/s41588-023-01419-6","journal-title":"Nature Genetics"},{"key":"1604_CR15","doi-asserted-by":"publisher","first-page":"10924","DOI":"10.1093\/nar\/gkad840","volume":"51","author":"T Wang","year":"2023","unstructured":"Wang, T., He, W., Li, X., Zhang, C., He, H., Yuan, Q., Zhang, B., Zhang, H., Leng, Y., Wei, H., Xu, Q., Shi, C., Liu, X., Guo, M., Wang, X., Chen, W., Zhang, Z., Yang, L., Lv, Y., \u2026 Shang, L. (2023). A rice variation map derived from 10 548 rice accessions reveals the importance of rare variants. Nucleic Acids Research, 51, 10924\u201310933. https:\/\/doi.org\/10.1093\/nar\/gkad840","journal-title":"Nucleic Acids Research"},{"key":"1604_CR16","doi-asserted-by":"publisher","DOI":"10.1016\/j.xplc.2024.101230","author":"W He","year":"2025","unstructured":"He, W., Li, X., Qian, Q., & Shang, L. (2025). The developments and prospects of plant super-pangenomes: Demands, approaches, and applications. Plant Communications. https:\/\/doi.org\/10.1016\/j.xplc.2024.101230","journal-title":"Plant Communications"},{"key":"1604_CR17","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.tplants.2019.10.012","volume":"25","author":"AW Khan","year":"2020","unstructured":"Khan, A. W., Garg, V., Roorkiwal, M., Golicz, A. A., Edwards, D., & Varshney, R. K. (2020). Super-pangenome by integrating the wild side of a species for accelerated crop improvement. Trends in Plant Science, 25, 148\u2013158. https:\/\/doi.org\/10.1016\/j.tplants.2019.10.012","journal-title":"Trends in Plant Science"},{"issue":"2005","key":"1604_CR18","doi-asserted-by":"publisher","first-page":"13950","DOI":"10.1073\/pnas.0506758102","volume":"102","author":"H Tettelin","year":"2005","unstructured":"Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C., Medini, D., Ward, N. L., Angiuoli, S. V., Crabtree, J., Jones, A. L., Durkin, A. S., DeBoy, R. T., Davidsen, T. M., Mora, M., Scarselli, M., MargarityRos, I., Peterson, J. D., Hauser, C. R., Sundaram, J. P., Nelson, W. C., & Fraser, C. M. (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial \u201cpan-genome.\u201d Proedings of the National Academy of Sciences, 102(2005), 13950\u201313955. https:\/\/doi.org\/10.1073\/pnas.0506758102","journal-title":"Proedings of the National Academy of Sciences"},{"key":"1604_CR19","doi-asserted-by":"publisher","first-page":"e000243","DOI":"10.1099\/mgen.0.000243","volume":"5","author":"CGP McCarthy","year":"2019","unstructured":"McCarthy, C. G. P., & Fitzpatrick, D. A. (2019). Pan-genome analyses of model fungal species. Microb Genom, 5, e000243. https:\/\/doi.org\/10.1099\/mgen.0.000243","journal-title":"Microb Genom"},{"key":"1604_CR20","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1038\/s41586-023-05896-x","volume":"617","author":"W-W Liao","year":"2023","unstructured":"Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., Buonaiuto, S., Chang, X. H., Cheng, H., Chu, J., Colonna, V., Eizenga, J. M., Feng, X., Fischer, C., Fulton, R. S., & Paten, B. (2023). A draft human pangenome reference. Nature, 617, 312\u2013324. https:\/\/doi.org\/10.1038\/s41586-023-05896-x","journal-title":"Nature"},{"key":"1604_CR21","doi-asserted-by":"publisher","first-page":"13390","DOI":"10.1038\/ncomms13390","volume":"7","author":"AA Golicz","year":"2016","unstructured":"Golicz, A. A., Bayer, P. E., Barker, G. C., Edger, P. P., Kim, H., Martinez, P. A., Chan, C. K. K., Severn-Ellis, A., McCombie, W. R., Parkin, I. A. P., Paterson, A. H., Pires, J. C., Sharpe, A. G., Tang, H., Teakle, G. R., Town, C. D., Batley, J., & Edwards, D. (2016). The pangenome of an agronomically important crop plant Brassica oleracea. Nature Communications, 7, 13390. https:\/\/doi.org\/10.1038\/ncomms13390","journal-title":"Nature Communications"},{"key":"1604_CR22","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1038\/nbt.2979","volume":"32","author":"Y Li","year":"2014","unstructured":"Li, Y., Zhou, G., Ma, J., Jiang, W., Jin, L., Zhang, Z., Guo, Y., Zhang, J., Sui, Y., Zheng, L., Zhang, S., Zuo, Q., Shi, X., Li, Y., Zhang, W., Hu, Y., Kong, G., Hong, H., Tan, B., \u2026 Qiu, L. (2014). De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nature Biotechnology, 32, 1045\u20131052. https:\/\/doi.org\/10.1038\/nbt.2979","journal-title":"Nature Biotechnology"},{"key":"1604_CR23","doi-asserted-by":"publisher","first-page":"3542","DOI":"10.1016\/j.cell.2021.04.046","volume":"184","author":"P Qin","year":"2021","unstructured":"Qin, P., Lu, H., Du, H., Wang, H., Chen, W., Chen, Z., He, Q., Ou, S., Zhang, H., Li, X., Li, X., Li, Y., Liao, Y., Gao, Q., Tu, B., Yuan, H., Ma, B., Wang, Y., Qian, Y., \u2026 Li, S. (2021). Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell, 184, 3542-3558.e16. https:\/\/doi.org\/10.1016\/j.cell.2021.04.046","journal-title":"Cell"},{"key":"1604_CR24","doi-asserted-by":"publisher","first-page":"878","DOI":"10.1038\/s41422-022-00685-z","volume":"32","author":"L Shang","year":"2022","unstructured":"Shang, L., Li, X., He, H., Yuan, Q., Song, Y., Wei, Z., Lin, H., Hu, M., Zhao, F., Zhang, C., Li, Y., Gao, H., Wang, T., Liu, X., Zhang, H., Zhang, Y., Cao, S., Yu, X., Zhang, B., \u2026 Qian, Q. (2022). A super pan-genomic landscape of rice. Cell Research, 32, 878\u2013896. https:\/\/doi.org\/10.1038\/s41422-022-00685-z","journal-title":"Cell Research"},{"key":"1604_CR25","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1111\/tpj.13515","volume":"90","author":"JD Montenegro","year":"2017","unstructured":"Montenegro, J. D., Golicz, A. A., Bayer, P. E., Hurgobin, B., Lee, H., Chan, C.-K.K., Visendi, P., Lai, K., Dole\u017eel, J., Batley, J., & Edwards, D. (2017). The pangenome of hexaploid bread wheat. The Plant Journal, 90, 1007\u20131013. https:\/\/doi.org\/10.1111\/tpj.13515","journal-title":"The Plant Journal"},{"key":"1604_CR26","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1038\/s41586-020-2961-x","volume":"588","author":"S Walkowiak","year":"2020","unstructured":"Walkowiak, S., Gao, L., Monat, C., Haberer, G., Kassa, M. T., Brinton, J., Ramirez-Gonzalez, R. H., Kolodziej, M. C., Delorean, E., Thambugala, D., Klymiuk, V., Byrns, B., Gundlach, H., Bandi, V., Siri, J. N., Nilsen, K., Aquino, C., Himmelbach, A., Copetti, D., & Pozniak, C. J. (2020). Multiple wheat genomes reveal global variation in modern breeding. Nature, 588, 277\u2013283. https:\/\/doi.org\/10.1038\/s41586-020-2961-x","journal-title":"Nature"},{"key":"1604_CR27","doi-asserted-by":"publisher","first-page":"2831","DOI":"10.1038\/s41588-025-02378-w","volume":"57","author":"S Yang","year":"2025","unstructured":"Yang, S., Wang, Y., Huang, Q., Wang, M., Wang, S., Fu, X., Zhu, C., Cheng, J., Liu, S., Yang, Z., Yang, N., Yan, J., Yang, X., & Qin, F. (2025). A pangenome of maize provides genetic insights into drought resistance. Nature Genetics, 57, 2831\u20132841. https:\/\/doi.org\/10.1038\/s41588-025-02378-w","journal-title":"Nature Genetics"},{"key":"1604_CR28","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2021.666342","volume":"12","author":"P Ruperao","year":"2021","unstructured":"Ruperao, P., Thirunavukkarasu, N., Gandham, P., Selvanayagam, S., Govindaraj, M., Nebie, B., Manyasa, E., Gupta, R., Das, R. R., Odeny, D. A., Gandhi, H., Edwards, D., Deshpande, S. P., & Rathore, A. (2021). Sorghum pan-genome explores the functional utility for genomic-assisted breeding to accelerate the genetic gain. Frontiers in Plant Science, 12, Article 666342. https:\/\/doi.org\/10.3389\/fpls.2021.666342","journal-title":"Frontiers in Plant Science"},{"key":"1604_CR29","doi-asserted-by":"publisher","first-page":"1044","DOI":"10.1038\/s41588-019-0410-2","volume":"51","author":"L Gao","year":"2019","unstructured":"Gao, L., Gonda, I., Sun, H., Ma, Q., Bao, K., Tieman, D. M., Burzynski-Chang, E. A., Fish, T. L., Stromberg, K. A., Sacks, G. L., Thannhauser, T. W., Foolad, M. R., Diez, M. J., Blanca, J., Canizares, J., Xu, Y., van der Knaap, E., Huang, S., Klee, H. J., \u2026 Fei, Z. (2019). The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nature Genetics, 51, 1044\u20131051. https:\/\/doi.org\/10.1038\/s41588-019-0410-2","journal-title":"Nature Genetics"},{"key":"1604_CR30","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/j.cell.2020.05.021","volume":"182","author":"M Alonge","year":"2020","unstructured":"Alonge, M., Wang, X., Benoit, M., Soyk, S., Pereira, L., Zhang, L., Suresh, H., Ramakrishnan, S., Maumus, F., Ciren, D., Levy, Y., Harel, T. H., Shalev-Schlosser, G., Amsellem, Z., Razifard, H., Caicedo, A. L., Tieman, D. M., Klee, H., Kirsche, M., & Lippman, Z. B. (2020). Major impacts of widespread structural variation on gene expression and crop improvement in tomato. Cell, 182, 145-161.e23. https:\/\/doi.org\/10.1016\/j.cell.2020.05.021","journal-title":"Cell"},{"key":"1604_CR31","doi-asserted-by":"publisher","first-page":"654","DOI":"10.1038\/s41586-024-08187-1","volume":"636","author":"M Jayakodi","year":"2024","unstructured":"Jayakodi, M., Lu, Q., Pidon, H., Rabanus-Wallace, M. T., Bayer, M., Lux, T., Guo, Y., Jaegle, B., Badea, A., Bekele, W., Brar, G. S., Braune, K., Bunk, B., Chalmers, K. J., Chapman, B., J\u00f8rgensen, M. E., Feng, J.-W., Feser, M., Fiebig, A., & Stein, N. (2024). Structural variation in the pangenome of wild and domesticated barley. Nature, 636, 654\u2013662. https:\/\/doi.org\/10.1038\/s41586-024-08187-1","journal-title":"Nature"},{"key":"1604_CR32","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1038\/s41477-019-0577-7","volume":"6","author":"J-M Song","year":"2020","unstructured":"Song, J.-M., Guan, Z., Hu, J., Guo, C., Yang, Z., Wang, S., Liu, D., Wang, B., Lu, S., Zhou, R., Xie, W.-Z., Cheng, Y., Zhang, Y., Liu, K., Yang, Q.-Y., Chen, L.-L., & Guo, L. (2020). Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nature Plants, 6, 34\u201345. https:\/\/doi.org\/10.1038\/s41477-019-0577-7","journal-title":"Nature Plants"},{"key":"1604_CR33","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1126\/science.abg5289","volume":"373","author":"MB Hufford","year":"2021","unstructured":"Hufford, M. B., Seetharam, A. S., Woodhouse, M. R., Chougule, K. M., Ou, S., Liu, J., Ricci, W. A., Guo, T., Olson, A., Qiu, Y., Della Coletta, R., Tittes, S., Hudson, A. I., Marand, A. P., Wei, S., Lu, Z., Wang, B., Tello-Ruiz, M. K., Piri, R. D., & Dawe, R. K. (2021). De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science, 373, 655\u2013662. https:\/\/doi.org\/10.1126\/science.abg5289","journal-title":"Science"},{"key":"1604_CR34","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1105\/tpc.113.119982","volume":"26","author":"CN Hirsch","year":"2014","unstructured":"Hirsch, C. N., Foerster, J. M., Johnson, J. M., Sekhon, R. S., Muttoni, G., Vaillancourt, B., Pe\u00f1agaricano, F., Lindquist, E., Pedraza, M. A., Barry, K., de Leon, N., Kaeppler, S. M., & Buell, C. R. (2014). Insights into the maize pan-genome and pan-transcriptome. The Plant Cell, 26, 121\u2013135. https:\/\/doi.org\/10.1105\/tpc.113.119982","journal-title":"The Plant Cell"},{"key":"1604_CR35","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/s13059-021-02351-w","volume":"22","author":"J Li","year":"2021","unstructured":"Li, J., Yuan, D., Wang, P., Wang, Q., Sun, M., Liu, Z., Si, H., Xu, Z., Ma, Y., Zhang, B., Pei, L., Tu, L., Zhu, L., Chen, L.-L., Lindsey, K., Zhang, X., Jin, S., & Wang, M. (2021). Cotton pan-genome retrieves the lost sequences and genes during domestication and selection. Genome Biology, 22, 119. https:\/\/doi.org\/10.1186\/s13059-021-02351-w","journal-title":"Genome Biology"},{"key":"1604_CR36","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1016\/j.molp.2022.01.003","volume":"15","author":"G Hoopes","year":"2022","unstructured":"Hoopes, G., Meng, X., Hamilton, J. P., Achakkagari, S. R., Guesdes, FdeAF., Bolger, M. E., Coombs, J. J., Esselink, D., Kaiser, N. R., Kodde, L., Kyriakidou, M., Lavrijssen, B., Lieshout, N., Shereda, R., Tuttle, H. K., Vaillancourt, B., Wood, J. C., Boer, JMde, Bornowski, N., & Finkers, R. (2022). Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Molecular Plant, 15, 520\u2013536. https:\/\/doi.org\/10.1016\/j.molp.2022.01.003","journal-title":"Molecular Plant"},{"key":"1604_CR37","doi-asserted-by":"publisher","DOI":"10.1016\/j.xplc.2022.100352","author":"C Liu","year":"2022","unstructured":"Liu, C., Wang, Y., Peng, J., Fan, B., Xu, D., Wu, J., Cao, Z., Gao, Y., Wang, X., Li, S., Su, Q., Zhang, Z., Wang, S., Wu, X., Shang, Q., Shi, H., Shen, Y., Wang, B., & Tian, J. (2022). High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement. Plant Communications. https:\/\/doi.org\/10.1016\/j.xplc.2022.100352","journal-title":"Plant Communications"},{"key":"1604_CR38","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1016\/j.cell.2020.05.023","volume":"182","author":"Y Liu","year":"2020","unstructured":"Liu, Y., Du, H., Li, P., Shen, Y., Peng, H., Liu, S., Zhou, G.-A., Zhang, H., Liu, Z., Shi, M., Huang, X., Li, Y., Zhang, M., Wang, Z., Zhu, B., Han, B., Liang, C., & Tian, Z. (2020). Pan-genome of wild and cultivated soybeans. Cell, 182, 162-176.e13. https:\/\/doi.org\/10.1016\/j.cell.2020.05.023","journal-title":"Cell"},{"key":"1604_CR39","doi-asserted-by":"publisher","first-page":"2247","DOI":"10.1038\/s41588-024-01901-9","volume":"56","author":"C Zhang","year":"2024","unstructured":"Zhang, C., Shao, Z., Kong, Y., Du, H., Li, W., Yang, Z., Li, X., Ke, H., Sun, Z., Shao, J., Chen, S., Zhang, H., Chu, J., Xing, X., Tian, R., Qin, N., Li, J., Huang, M., Sun, Y., & Li, X. (2024). High-quality genome of a modern soybean cultivar and resequencing of 547 accessions provide insights into the role of structural variation. Nature Genetics, 56, 2247\u20132258. https:\/\/doi.org\/10.1038\/s41588-024-01901-9","journal-title":"Nature Genetics"},{"key":"1604_CR40","doi-asserted-by":"publisher","first-page":"1503","DOI":"10.1016\/j.molp.2022.08.006","volume":"15","author":"H Liu","year":"2022","unstructured":"Liu, H., Wang, X., Liu, S., Huang, Y., Guo, Y.-X., Xie, W.-Z., Liu, H., ul Qamar, M. T., Xu, Q., & Chen, L.-L. (2022). Citrus pan-genome to breeding database (CPBD): A comprehensive genome database for citrus breeding. Molecular Plant, 15, 1503\u20131505. https:\/\/doi.org\/10.1016\/j.molp.2022.08.006","journal-title":"Molecular Plant"},{"key":"1604_CR41","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14779-y","volume":"11","author":"W-B Jiao","year":"2020","unstructured":"Jiao, W.-B., & Schneeberger, K. (2020). Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nature Communications, 11, Article 989. https:\/\/doi.org\/10.1038\/s41467-020-14779-y","journal-title":"Nature Communications"},{"key":"1604_CR42","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-42029-4","volume":"14","author":"M Kang","year":"2023","unstructured":"Kang, M., Wu, H., Liu, H., Liu, W., Zhu, M., Han, Y., Liu, W., Chen, C., Song, Y., Tan, L., Yin, K., Zhao, Y., Yan, Z., Lou, S., Zan, Y., & Liu, J. (2023). The pan-genome and local adaptation of Arabidopsis thaliana. Nature Communications, 14, Article 6259. https:\/\/doi.org\/10.1038\/s41467-023-42029-4","journal-title":"Nature Communications"},{"key":"1604_CR43","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1038\/s41477-020-0733-0","volume":"6","author":"PE Bayer","year":"2020","unstructured":"Bayer, P. E., Golicz, A. A., Scheben, A., Batley, J., & Edwards, D. (2020). Plant pan-genomes are the new reference. Nature Plants, 6, 914\u2013920. https:\/\/doi.org\/10.1038\/s41477-020-0733-0","journal-title":"Nature Plants"},{"key":"1604_CR44","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1016\/j.pbi.2019.12.010","volume":"54","author":"H Wang","year":"2020","unstructured":"Wang, H., Cimen, E., Singh, N., & Buckler, E. (2020). Deep learning for plant genomics and crop improvement. Current Opinion in Plant Biology, 54, 34\u201341. https:\/\/doi.org\/10.1016\/j.pbi.2019.12.010","journal-title":"Current Opinion in Plant Biology"},{"key":"1604_CR45","doi-asserted-by":"publisher","DOI":"10.1002\/tpg2.20112","volume":"14","author":"PE Bayer","year":"2021","unstructured":"Bayer, P. E., Petereit, J., Danilevicz, M. F., Anderson, R., Batley, J., & Edwards, D. (2021). The application of pangenomics and machine learning in genomic selection in plants. The Plant Genome, 14, Article e20112. https:\/\/doi.org\/10.1002\/tpg2.20112","journal-title":"The Plant Genome"},{"key":"1604_CR46","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1038\/s41477-024-01902-w","volume":"11","author":"Y Li","year":"2025","unstructured":"Li, Y., Zhang, B., Zhang, S., Wong, C. E., Liang, Q., Pang, S., Wu, Y., Zhao, M., & Yu, H. (2025). Pangeneric genome analyses reveal the evolution and diversity of the orchid genus Dendrobium. Nature Plants, 11, 421\u2013437. https:\/\/doi.org\/10.1038\/s41477-024-01902-w","journal-title":"Nature Plants"},{"key":"1604_CR47","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1534\/g3.119.300585","volume":"9","author":"OA Montesinos-L\u00f3pez","year":"2019","unstructured":"Montesinos-L\u00f3pez, O. A., Mart\u00edn-Vallejo, J., Crossa, J., Gianola, D., Hern\u00e1ndez-Su\u00e1rez, C. M., Montesinos-L\u00f3pez, A., Juliana, P., & Singh, R. (2019). New deep learning genomic-based prediction model for multiple traits with binary, ordinal, and continuous phenotypes. G3, Genes|Genomes|Genetics, 9, 1545\u20131556. https:\/\/doi.org\/10.1534\/g3.119.300585","journal-title":"G3, Genes|Genomes|Genetics"},{"key":"1604_CR48","doi-asserted-by":"publisher","DOI":"10.1038\/s44383-025-00019-z","volume":"2","author":"A Raza","year":"2026","unstructured":"Raza, A., Li, Y., Jan, F., Fernandez, C. G. T., Mir, R. R., Hu, Z., & Varshney, R. K. (2026). From the genome to super-pangenome: A new paradigm for accelerated crop improvement. NPJ Science of Plants, 2, Article 4. https:\/\/doi.org\/10.1038\/s44383-025-00019-z","journal-title":"NPJ Science of Plants"},{"key":"1604_CR49","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1038\/s41576-024-00691-4","volume":"25","author":"M Schreiber","year":"2024","unstructured":"Schreiber, M., Jayakodi, M., Stein, N., & Mascher, M. (2024). Plant pangenomes for crop improvement, biodiversity and evolution. Nature Reviews Genetics, 25, 563\u2013577. https:\/\/doi.org\/10.1038\/s41576-024-00691-4","journal-title":"Nature Reviews Genetics"},{"key":"1604_CR50","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41588-023-01340-y","volume":"55","author":"N Li","year":"2023","unstructured":"Li, N., He, Q., Wang, J., Wang, B., Zhao, J., Huang, S., Yang, T., Tang, Y., Yang, S., Aisimutuola, P., Xu, R., Hu, J., Jia, C., Ma, K., Li, Z., Jiang, F., Gao, J., Lan, H., Zhou, Y., \u2026 Yu, Q. (2023). Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nature Genetics, 55, 852\u2013860. https:\/\/doi.org\/10.1038\/s41588-023-01340-y","journal-title":"Nature Genetics"},{"key":"1604_CR51","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1186\/s13059-020-02168-z","volume":"21","author":"H Li","year":"2020","unstructured":"Li, H., Feng, X., & Chu, C. (2020). The design and construction of reference pangenome graphs with minigraph. Genome Biology, 21, 265. https:\/\/doi.org\/10.1186\/s13059-020-02168-z","journal-title":"Genome Biology"},{"key":"1604_CR52","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0506-z","volume":"15","author":"MC Schatz","year":"2014","unstructured":"Schatz, M. C., Maron, L. G., Stein, J. C., Wences, A. H., Gurtowski, J., Biggers, E., Lee, H., Kramer, M., Antoniou, E., Ghiban, E., Wright, M. H., Chia, J., Ware, D., McCouch, S. R., & McCombie, W. R. (2014). Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biology, 15, Article 506. https:\/\/doi.org\/10.1186\/s13059-014-0506-z","journal-title":"Genome Biology"},{"key":"1604_CR53","doi-asserted-by":"publisher","first-page":"1938","DOI":"10.1007\/s11427-020-1808-0","volume":"63","author":"Y Liu","year":"2020","unstructured":"Liu, Y., & Tian, Z. (2020). From one linear genome to a graph-based pan-genome: A new era for genomics. Science China. Life Sciences, 63, 1938\u20131941. https:\/\/doi.org\/10.1007\/s11427-020-1808-0","journal-title":"Science China. Life Sciences"},{"key":"1604_CR54","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1007\/s42994-025-00206-7","volume":"6","author":"Z-Z Du","year":"2025","unstructured":"Du, Z.-Z., He, J.-B., & Jiao, W.-B. (2025). Plant graph-based pangenomics: Techniques, applications, and challenges. aBIOTECH, 6, 361\u2013376. https:\/\/doi.org\/10.1007\/s42994-025-00206-7","journal-title":"aBIOTECH"},{"key":"1604_CR55","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1038\/s41586-018-0063-9","volume":"557","author":"W Wang","year":"2018","unstructured":"Wang, W., Mauleon, R., Hu, Z., Chebotarov, D., Tai, S., Wu, Z., Li, M., Zheng, T., Fuentes, R. R., Zhang, F., Mansueto, L., Copetti, D., Sanciangco, M., Palis, K. C., Xu, J., Sun, C., Fu, B., Zhang, H., Gao, Y., & Leung, H. (2018). Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 557, 43\u201349. https:\/\/doi.org\/10.1038\/s41586-018-0063-9","journal-title":"Nature"},{"key":"1604_CR56","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1038\/s41586-021-04066-1","volume":"599","author":"RK Varshney","year":"2021","unstructured":"Varshney, R. K., Roorkiwal, M., Sun, S., Bajaj, P., Chitikineni, A., Thudi, M., Singh, N. P., Du, X., Upadhyaya, H. D., Khan, A. W., Wang, Y., Garg, V., Fan, G., Cowling, W. A., Crossa, J., Gentzbittel, L., Voss-Fels, K. P., Valluri, V. K., Sinha, P., & Liu, X. (2021). A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature, 599, 622\u2013627. https:\/\/doi.org\/10.1038\/s41586-021-04066-1","journal-title":"Nature"},{"key":"1604_CR57","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1038\/s41477-022-01102-4","volume":"8","author":"Y Zhuang","year":"2022","unstructured":"Zhuang, Y., Wang, X., Li, X., Hu, J., Fan, L., Landis, J. B., Cannon, S. B., Grimwood, J., Schmutz, J., Jackson, S. A., Doyle, J. J., Zhang, X. S., Zhang, D., & Ma, J. (2022). Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition. Nature Plants, 8, 233\u2013244. https:\/\/doi.org\/10.1038\/s41477-022-01102-4","journal-title":"Nature Plants"},{"key":"1604_CR58","doi-asserted-by":"publisher","first-page":"2408","DOI":"10.1093\/bioinformatics\/btx170","volume":"33","author":"Z Hu","year":"2017","unstructured":"Hu, Z., Sun, C., Lu, K.-C., Chu, X., Zhao, Y., Lu, J., Shi, J., & Wei, C. (2017). EUPAN enables pan-genome studies of a large number of eukaryotic genomes. Bioinformatics, 33, 2408\u20132409. https:\/\/doi.org\/10.1093\/bioinformatics\/btx170","journal-title":"Bioinformatics"},{"key":"1604_CR59","doi-asserted-by":"publisher","first-page":"1553","DOI":"10.1038\/s41588-022-01172-2","volume":"54","author":"T Yang","year":"2022","unstructured":"Yang, T., Liu, R., Luo, Y., Hu, S., Wang, D., Wang, C., Pandey, M. K., Ge, S., Xu, Q., Li, N., Li, G., Huang, Y., Saxena, R. K., Ji, Y., Li, M., Yan, X., He, Y., Liu, Y., Wang, X., \u2026 Zong, X. (2022). Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nature Genetics, 54, 1553\u20131563. https:\/\/doi.org\/10.1038\/s41588-022-01172-2","journal-title":"Nature Genetics"},{"key":"1604_CR60","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2211117120","volume":"120","author":"I Bozan","year":"2023","unstructured":"Bozan, I., Achakkagari, S. R., Anglin, N. L., Ellis, D., Tai, H. H., & Str\u00f6mvik, M. V. (2023). Pangenome analyses reveal impact of transposable elements and ploidy on the evolution of potato species. Proceedings of the National Academy of Sciences of the United States of America, 120, Article e2211117120. https:\/\/doi.org\/10.1073\/pnas.2211117120","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"1604_CR61","doi-asserted-by":"publisher","DOI":"10.1016\/j.xplc.2023.100729","author":"H Miao","year":"2024","unstructured":"Miao, H., Wang, L., Qu, L., Liu, H., Sun, Y., Le, M., Wang, Q., Wei, S., Zheng, Y., Lin, W., Duan, Y., Cao, H., Xiong, S., Wang, X., Wei, L., Li, C., Ma, Q., Ju, M., Zhao, R., & Zhang, H. (2024). Genomic evolution and insights into agronomic trait innovations of Sesamum species. Plant Communications. https:\/\/doi.org\/10.1016\/j.xplc.2023.100729","journal-title":"Plant Communications"},{"key":"1604_CR62","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1016\/j.molp.2024.03.009","volume":"17","author":"T Shi","year":"2024","unstructured":"Shi, T., Zhang, X., Hou, Y., Jia, C., Dan, X., Zhang, Y., Jiang, Y., Lai, Q., Feng, J., Feng, J., Ma, T., Wu, J., Liu, S., Zhang, L., Long, Z., Chen, L., Street, N. R., Ingvarsson, P. K., Liu, J., & Wang, T. (2024). The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees. Molecular Plant, 17, 725\u2013746. https:\/\/doi.org\/10.1016\/j.molp.2024.03.009","journal-title":"Molecular Plant"},{"key":"1604_CR63","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1038\/s41588-025-02111-7","volume":"57","author":"L Guo","year":"2025","unstructured":"Guo, L., Wang, X., Ayhan, D. H., Rhaman, M. S., Yan, M., Jiang, J., Wang, D., Zheng, W., Mei, J., Ji, W., Jiao, J., Chen, S., Sun, J., Yi, S., Meng, D., Wang, J., Bhuiyan, M. N., Qin, G., Guo, L., & Ye, W. (2025). Super pangenome of Vitis empowers identification of downy mildew resistance genes for grapevine improvement. Nature Genetics, 57, 741\u2013753. https:\/\/doi.org\/10.1038\/s41588-025-02111-7","journal-title":"Nature Genetics"},{"key":"1604_CR64","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-025-02294-z","author":"H Zhang","year":"2025","unstructured":"Zhang, H., Liu, N., Wang, Y., Zheng, X., Li, W., Liu, Z., Liu, J., Wang, Y., Xing, L., Li, T., Yun, Y., Zhou, Q., Wang, M., Qin, Y., Yan, J., Gong, Z., He, Q., & Du, H. (2025). Super-pangenome analyses across 35 accessions of 23 Avena species highlight their complex evolutionary history and extensive genomic diversity. Nat Genet. https:\/\/doi.org\/10.1038\/s41588-025-02294-z","journal-title":"Nat Genet"},{"key":"1604_CR65","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1093\/jxb\/erac412","volume":"74","author":"S Wang","year":"2023","unstructured":"Wang, S., Qian, Y.-Q., Zhao, R.-P., Chen, L.-L., & Song, J.-M. (2023). Graph-based pan-genomes: Increased opportunities in plant genomics. Journal of Experimental Botany, 74, 24\u201339. https:\/\/doi.org\/10.1093\/jxb\/erac412","journal-title":"Journal of Experimental Botany"},{"key":"1604_CR66","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1186\/s13059-022-02742-7","volume":"23","author":"S Gui","year":"2022","unstructured":"Gui, S., Wei, W., Jiang, C., Luo, J., Chen, L., Wu, S., Li, W., Wang, Y., Li, S., Yang, N., Li, Q., Fernie, A. R., & Yan, J. (2022). A pan-Zea genome map for enhancing maize improvement. Genome Biology, 23, 178. https:\/\/doi.org\/10.1186\/s13059-022-02742-7","journal-title":"Genome Biology"},{"key":"1604_CR67","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1016\/j.molp.2023.02.004","volume":"16","author":"S Jin","year":"2023","unstructured":"Jin, S., Han, Z., Hu, Y., Si, Z., Dai, F., He, L., Cheng, Y., Li, Y., Zhao, T., Fang, L., & Zhang, T. (2023). Structural variation (SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons. Molecular Plant, 16, 678\u2013693. https:\/\/doi.org\/10.1016\/j.molp.2023.02.004","journal-title":"Molecular Plant"},{"key":"1604_CR68","doi-asserted-by":"publisher","first-page":"1225","DOI":"10.1038\/s41588-024-01760-4","volume":"56","author":"AW Khan","year":"2024","unstructured":"Khan, A. W., Garg, V., Sun, S., Gupta, S., Dudchenko, O., Roorkiwal, M., Chitikineni, A., Bayer, P. E., Shi, C., Upadhyaya, H. D., Bohra, A., Bharadwaj, C., Mir, R. R., Baruch, K., Yang, B., Coyne, C. J., Bansal, K. C., Nguyen, H. T., Ronen, G., & Varshney, R. K. (2024). Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea. Nature Genetics, 56, 1225\u20131234. https:\/\/doi.org\/10.1038\/s41588-024-01760-4","journal-title":"Nature Genetics"},{"key":"1604_CR69","doi-asserted-by":"publisher","first-page":"527","DOI":"10.1038\/s41586-022-04808-9","volume":"606","author":"Y Zhou","year":"2022","unstructured":"Zhou, Y., Zhang, Z., Bao, Z., Li, H., Lyu, Y., Zan, Y., Wu, Y., Cheng, L., Fang, Y., Wu, K., Zhang, J., Lyu, H., Lin, T., Gao, Q., Saha, S., Mueller, L., Fei, Z., St\u00e4dler, T., Xu, S., & Huang, S. (2022). Graph pangenome captures missing heritability and empowers tomato breeding. Nature, 606, 527\u2013534. https:\/\/doi.org\/10.1038\/s41586-022-04808-9","journal-title":"Nature"},{"key":"1604_CR70","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1016\/j.molp.2025.01.017","volume":"18","author":"X Zhu","year":"2025","unstructured":"Zhu, X., Yang, R., Liang, Q., Yu, Y., Wang, T., Meng, L., Wang, P., Wang, S., Li, X., Yang, Q., Guo, H., Sui, Q., Wang, Q., Du, H., Chen, Q., Liang, Z., Wu, X., Zeng, Q., & Huang, B. (2025). Graph-based pangenome provides insights into structural variations and genetic basis of metabolic traits in potato. Molecular Plant, 18, 590\u2013602. https:\/\/doi.org\/10.1016\/j.molp.2025.01.017","journal-title":"Molecular Plant"},{"key":"1604_CR71","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-024-05712-2","volume":"24","author":"D-JM van Workum","year":"2024","unstructured":"van Workum, D.-J.M., Mehrem, S. L., Snoek, B. L., Alderkamp, M. C., Lapin, D., Mulder, F. F. M., Van den Ackerveken, G., de Ridder, D., Schranz, M. E., & Smit, S. (2024). Lactuca super-pangenome reduces bias towards reference genes in lettuce research. BMC Plant Biology, 24, Article 1019. https:\/\/doi.org\/10.1186\/s12870-024-05712-2","journal-title":"BMC Plant Biology"},{"key":"1604_CR72","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-62641-w","volume":"16","author":"S Cao","year":"2025","unstructured":"Cao, S., Sawettalake, N., & Shen, L. (2025). Lactuca super-pangenome provides insights into lettuce genome evolution and domestication. Nature Communications, 16, Article 7257. https:\/\/doi.org\/10.1038\/s41467-025-62641-w","journal-title":"Nature Communications"},{"key":"1604_CR73","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1146\/annurev-arplant-080720-105454","volume":"72","author":"L Lei","year":"2021","unstructured":"Lei, L., Goltsman, E., Goodstein, D., Wu, G. A., Rokhsar, D. S., & Vogel, J. P. (2021). Plant pan-genomics comes of age. Annual Review of Plant Biology, 72, 411\u2013435. https:\/\/doi.org\/10.1146\/annurev-arplant-080720-105454","journal-title":"Annual Review of Plant Biology"},{"key":"1604_CR74","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1038\/s41467-022-28362-0","volume":"13","author":"H Li","year":"2022","unstructured":"Li, H., Wang, S., Chai, S., Yang, Z., Zhang, Q., Xin, H., Xu, Y., Lin, S., Chen, X., Yao, Z., Yang, Q., Fei, Z., Huang, S., & Zhang, Z. (2022). Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber. Nature Communications, 13, 682. https:\/\/doi.org\/10.1038\/s41467-022-28362-0","journal-title":"Nature Communications"},{"key":"1604_CR75","doi-asserted-by":"publisher","DOI":"10.1186\/1939-8433-6-4","volume":"6","author":"Y Kawahara","year":"2013","unstructured":"Kawahara, Y., de la BastideHamilton, M. J. P., Kanamori, H., McCombie, W. R., Ouyang, S., Schwartz, D. C., Tanaka, T., Wu, J., Zhou, S., Childs, K. L., Davidson, R. M., Lin, H., Quesada-Ocampo, L., Vaillancourt, B., Sakai, H., Lee, S. S., Kim, J., Numa, H., & Matsumoto, T. (2013). Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice, 6, Article 4. https:\/\/doi.org\/10.1186\/1939-8433-6-4","journal-title":"Rice"},{"key":"1604_CR76","doi-asserted-by":"publisher","first-page":"1750","DOI":"10.1038\/s41588-024-01823-6","volume":"56","author":"Y Zhang","year":"2024","unstructured":"Zhang, Y., Zhao, M., Tan, J., Huang, M., Chu, X., Li, Y., Han, X., Fang, T., Tian, Y., Jarret, R., Lu, D., Chen, Y., Xue, L., Li, X., Qin, G., Li, B., Sun, Y., Deng, X. W., Deng, Y., \u2026 He, H. (2024). Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nature Genetics, 56, 1750\u20131761. https:\/\/doi.org\/10.1038\/s41588-024-01823-6","journal-title":"Nature Genetics"},{"key":"1604_CR77","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-026-10105-6","author":"H Cheng","year":"2026","unstructured":"Cheng, H., Qu, H., McKenzie, S., Lawrence, K. R., Windsor, R., Vella, M., Park, P. J., & Li, H. (2026). Efficient near-telomere-to-telomere assembly of nanopore simplex reads. Nature. https:\/\/doi.org\/10.1038\/s41586-026-10105-6","journal-title":"Nature"},{"key":"1604_CR78","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1016\/j.tplants.2025.11.002","volume":"31","author":"J Zhang","year":"2026","unstructured":"Zhang, J., Zheng, Y., & Chen, F. (2026). Phased telomere-to-telomere super-pangenome: Definitive reference genome in plants. Trends in Plant Science, 31, 266\u2013269. https:\/\/doi.org\/10.1016\/j.tplants.2025.11.002","journal-title":"Trends in Plant Science"},{"key":"1604_CR79","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1038\/s41588-018-0041-z","volume":"50","author":"Q Zhao","year":"2018","unstructured":"Zhao, Q., Feng, Q., Lu, H., Li, Y., Wang, A., Tian, Q., Zhan, Q., Lu, Y., Zhang, L., Huang, T., Wang, Y., Fan, D., Zhao, Y., Wang, Z., Zhou, C., Chen, J., Zhu, C., Li, W., Weng, Q., & Huang, X. (2018). Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nature Genetics, 50, 278\u2013284. https:\/\/doi.org\/10.1038\/s41588-018-0041-z","journal-title":"Nature Genetics"},{"key":"1604_CR80","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1101\/gr.276015.121","volume":"32","author":"F Zhang","year":"2022","unstructured":"Zhang, F., Xue, H., Dong, X., Li, M., Zheng, X., Li, Z., Xu, J., Wang, W., & Wei, C. (2022). Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes. Genome Research, 32, 853\u2013863. https:\/\/doi.org\/10.1101\/gr.276015.121","journal-title":"Genome Research"},{"key":"1604_CR81","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-023-03017-5","volume":"24","author":"D Wu","year":"2023","unstructured":"Wu, D., Xie, L., Sun, Y., Huang, Y., Jia, L., Dong, C., Shen, E., Ye, C.-Y., Qian, Q., & Fan, L. (2023). A syntelog-based pan-genome provides insights into rice domestication and de-domestication. Genome Biology, 24, Article 179. https:\/\/doi.org\/10.1186\/s13059-023-03017-5","journal-title":"Genome Biology"},{"key":"1604_CR82","doi-asserted-by":"publisher","first-page":"766","DOI":"10.1038\/s41477-021-00925-x","volume":"7","author":"Y Tao","year":"2021","unstructured":"Tao, Y., Luo, H., Xu, J., Cruickshank, A., Zhao, X., Teng, F., Hathorn, A., Wu, X., Liu, Y., Shatte, T., Jordan, D., Jing, H., & Mace, E. (2021). Extensive variation within the pan-genome of cultivated and wild sorghum. Nature Plants, 7, 766\u2013773. https:\/\/doi.org\/10.1038\/s41477-021-00925-x","journal-title":"Nature Plants"},{"key":"1604_CR83","doi-asserted-by":"publisher","DOI":"10.1002\/tpg2.20109","volume":"15","author":"PE Bayer","year":"2022","unstructured":"Bayer, P. E., Valliyodan, B., Hu, H., Marsh, J. I., Yuan, Y., Vuong, T. D., Patil, G., Song, Q., Batley, J., Varshney, R. K., Lam, H.-M., Edwards, D., & Nguyen, H. T. (2022). Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding. The Plant Genome, 15, Article e20109. https:\/\/doi.org\/10.1002\/tpg2.20109","journal-title":"The Plant Genome"},{"key":"1604_CR84","doi-asserted-by":"publisher","first-page":"3783","DOI":"10.1111\/pbi.70199","volume":"23","author":"J Yu","year":"2025","unstructured":"Yu, J., Chen, Q., Yuan, L., Feng, S., Huang, M., Zheng, P., Chen, G., Tao, X., Edwards, D., Chen, Z.-H., & Xu, S. (2025). Phylogenomic and super-pangenome analyses unveil the genetic landscape of tomato evolution and domestication. Plant Biotechnology Journal, 23, 3783\u20133797. https:\/\/doi.org\/10.1111\/pbi.70199","journal-title":"Plant Biotechnology Journal"},{"key":"1604_CR85","doi-asserted-by":"publisher","first-page":"1959","DOI":"10.1038\/s41588-022-01237-2","volume":"54","author":"M Wang","year":"2022","unstructured":"Wang, M., Li, J., Qi, Z., Long, Y., Pei, L., Huang, X., Grover, C. E., Du, X., Xia, C., Wang, P., Liu, Z., You, J., Tian, X., Ma, Y., Wang, R., Chen, X., He, X., Fang, D. D., Sun, Y., \u2026 Zhang, X. (2022). Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium. Nature Genetics, 54, 1959\u20131971. https:\/\/doi.org\/10.1038\/s41588-022-01237-2","journal-title":"Nature Genetics"},{"key":"1604_CR86","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1186\/s12915-024-01893-2","volume":"22","author":"X He","year":"2024","unstructured":"He, X., Qi, Z., Liu, Z., Chang, X., Zhang, X., Li, J., & Wang, M. (2024). Pangenome analysis reveals transposon-driven genome evolution in cotton. BMC Biology, 22, 92. https:\/\/doi.org\/10.1186\/s12915-024-01893-2","journal-title":"BMC Biology"},{"key":"1604_CR87","doi-asserted-by":"publisher","DOI":"10.3390\/ijms25179677","volume":"25","author":"Y Song","year":"2024","unstructured":"Song, Y., Han, S., Wang, M., Ni, X., Huang, X., & Zhang, Y. (2024). Pangenome identification and analysis of terpene synthase gene family members in Gossypium. International Journal of Molecular Sciences, 25, Article 9677. https:\/\/doi.org\/10.3390\/ijms25179677","journal-title":"International Journal of Molecular Sciences"},{"key":"1604_CR88","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1186\/s13059-023-03133-2","volume":"24","author":"N Cochetel","year":"2023","unstructured":"Cochetel, N., Minio, A., Guarracino, A., Garcia, J. F., Figueroa-Balderas, R., Massonnet, M., Kasuga, T., Londo, J. P., Garrison, E., Gaut, B. S., & Cantu, D. (2023). A super-pangenome of the North American wild grape species. Genome Biology, 24, 290. https:\/\/doi.org\/10.1186\/s13059-023-03133-2","journal-title":"Genome Biology"},{"key":"1604_CR89","doi-asserted-by":"publisher","first-page":"2804","DOI":"10.1038\/s41588-024-01967-5","volume":"56","author":"Z Liu","year":"2024","unstructured":"Liu, Z., Wang, N., Su, Y., Long, Q., Peng, Y., Shangguan, L., Zhang, F., Cao, S., Wang, X., Ge, M., Xue, H., Ma, Z., Liu, W., Xu, X., Li, C., Cao, X., Ahmad, B., Su, X., Liu, Y., & Zhou, Y. (2024). Grapevine pangenome facilitates trait genetics and genomic breeding. Nature Genetics, 56, 2804\u20132814. https:\/\/doi.org\/10.1038\/s41588-024-01967-5","journal-title":"Nature Genetics"},{"key":"1604_CR90","doi-asserted-by":"publisher","DOI":"10.1002\/tpg2.20100","volume":"15","author":"H Rijzaani","year":"2022","unstructured":"Rijzaani, H., Bayer, P. E., Rouard, M., Dole\u017eel, J., Batley, J., & Edwards, D. (2022). The pangenome of banana highlights differences between genera and genomes. The Plant Genome, 15, Article e20100. https:\/\/doi.org\/10.1002\/tpg2.20100","journal-title":"The Plant Genome"},{"key":"1604_CR91","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-51031-3","volume":"15","author":"Y Fang","year":"2024","unstructured":"Fang, Y., Xiao, X., Lin, J., Lin, Q., Wang, J., Liu, K., Li, Z., Xing, J., Liu, Z., Wang, B., Qi, Y., Long, X., Zeng, X., Hu, Y., Qi, J., Qin, Y., Yang, J., Zhang, Y., Zhang, S., & Tang. (2024). Pan-genome and phylogenomic analyses highlight Hevea species delineation and rubber trait evolution. Nature Communications, 15, Article 7232. https:\/\/doi.org\/10.1038\/s41467-024-51031-3","journal-title":"Nature Communications"},{"key":"1604_CR92","doi-asserted-by":"publisher","first-page":"1423","DOI":"10.1038\/s41588-020-00723-9","volume":"52","author":"X Sun","year":"2020","unstructured":"Sun, X., Jiao, C., Schwaninger, H., Chao, C. T., Ma, Y., Duan, N., Khan, A., Ban, S., Xu, K., Cheng, L., Zhong, G.-Y., & Fei, Z. (2020). Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nature Genetics, 52, 1423\u20131432. https:\/\/doi.org\/10.1038\/s41588-020-00723-9","journal-title":"Nature Genetics"},{"key":"1604_CR93","doi-asserted-by":"publisher","first-page":"2799","DOI":"10.1093\/plphys\/kiae258","volume":"195","author":"Y Su","year":"2024","unstructured":"Su, Y., Yang, X., Wang, Y., Li, J., Long, Q., Cao, S., Wang, X., Liu, Z., Huang, S., Chen, Z., Peng, Y., Zhang, F., Xue, H., Cao, X., Zhang, M., Yisilam, G., Chu, Z., Gao, Y., Zhou, Y., & Tian, X. (2024). Phased telomere-to-telomere reference genome and pangenome reveal an expansion of resistance genes during apple domestication. Plant Physiology, 195, 2799\u20132814. https:\/\/doi.org\/10.1093\/plphys\/kiae258","journal-title":"Plant Physiology"},{"key":"1604_CR94","doi-asserted-by":"publisher","first-page":"e2105431118","DOI":"10.1073\/pnas.2105431118","volume":"118","author":"Q Qiao","year":"2021","unstructured":"Qiao, Q., Edger, P. P., Xue, L., Qiong, L., Lu, J., Zhang, Y., Cao, Q., Yocca, A. E., Platts, A. E., Knapp, S. J., Van Montagu, M., Van de Peer, Y., Lei, J., & Zhang, T. (2021). Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp). Proceedings of the National Academy of Sciences of the United States of America, 118, e2105431118. https:\/\/doi.org\/10.1073\/pnas.2105431118","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"1604_CR95","doi-asserted-by":"publisher","first-page":"1926","DOI":"10.1111\/pbi.14120","volume":"21","author":"S Wu","year":"2023","unstructured":"Wu, S., Sun, H., Gao, L., Branham, S., McGregor, C., Renner, S. S., Xu, Y., Kousik, C., Wechter, W. P., Levi, A., & Fei, Z. (2023). A Citrullus genus super-pangenome reveals extensive variations in wild and cultivated watermelons and sheds light on watermelon evolution and domestication. Plant Biotechnology Journal, 21, 1926\u20131928. https:\/\/doi.org\/10.1111\/pbi.14120","journal-title":"Plant Biotechnology Journal"},{"key":"1604_CR96","doi-asserted-by":"publisher","first-page":"1176","DOI":"10.1038\/s41588-026-02598-8","volume":"58","author":"H Sun","year":"2026","unstructured":"Sun, H., Zhang, J., Liao, S., Guo, S., Zhou, Z., Zhao, X., Wu, S., Zhao, J., Gong, G., Wang, J., Li, M., Yu, Y., Ren, Y., Tian, S., Li, S., Zhang, H., Hammar, S. A., McGregor, C., Jarret, R., & Xu, Y. (2026). Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon. Nature Genetics, 58, 1176\u20131185. https:\/\/doi.org\/10.1038\/s41588-026-02598-8","journal-title":"Nature Genetics"},{"key":"1604_CR97","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1186\/s12915-024-02002-z","volume":"22","author":"X Li","year":"2024","unstructured":"Li, X., Huo, L., Li, X., Zhang, C., Gu, M., Fan, J., Xu, C., Gong, J., Hu, X., Zheng, Y., & Sun, X. (2024). Genomes of diverse Actinidia species provide insights into cis-regulatory motifs and genes associated with critical traits. BMC Biology, 22, 200. https:\/\/doi.org\/10.1186\/s12915-024-02002-z","journal-title":"BMC Biology"},{"key":"1604_CR98","doi-asserted-by":"publisher","DOI":"10.1002\/advs.202400322","volume":"11","author":"Y Wang","year":"2024","unstructured":"Wang, Y., Li, P., Zhu, Y., Zhang, F., Zhang, S., He, Y., Wu, Y., Lin, Y., Wang, H., Ren, W., Wang, L., Yang, Y., Wang, R., Zheng, P., Liu, Y., Wang, S., & Yue, J. (2024). Graph-based pangenome of Actinidia chinensis reveals structural variations mediating fruit degreening. Advanced Science, 11, Article 2400322. https:\/\/doi.org\/10.1002\/advs.202400322","journal-title":"Advanced Science"},{"key":"1604_CR99","doi-asserted-by":"publisher","DOI":"10.1186\/s43897-024-00123-1","volume":"5","author":"X Yu","year":"2025","unstructured":"Yu, X., Qu, M., Wu, P., Zhou, M., Lai, E., Liu, H., Guo, S., Li, S., Yao, X., & Gao, L. (2025). Super pan-genome reveals extensive genomic variations associated with phenotypic divergence in Actinidia. Molecular Horticulture, 5, Article 4. https:\/\/doi.org\/10.1186\/s43897-024-00123-1","journal-title":"Molecular Horticulture"},{"key":"1604_CR100","doi-asserted-by":"publisher","DOI":"10.1093\/hr\/uhaf067","volume":"12","author":"H Wu","year":"2025","unstructured":"Wu, H., Yang, W., Dong, G., Hu, Q., Li, D., & Liu, J. (2025). Construction of the super pan-genome for the genus Actinidia reveals structural variations linked to phenotypic diversity. Horticulture Research, 12, Article uhaf067. https:\/\/doi.org\/10.1093\/hr\/uhaf067","journal-title":"Horticulture Research"},{"key":"1604_CR101","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1111\/nph.15413","volume":"220","author":"L Ou","year":"2018","unstructured":"Ou, L., Li, D., Lv, J., Chen, W., Zhang, Z., Li, X., Yang, B., Zhou, S., Yang, S., Li, W., Gao, H., Zeng, Q., Yu, H., Ouyang, B., Li, F., Liu, F., Zheng, J., Liu, Y., Wang, J., \u2026 Zou, X. (2018). Pan-genome of cultivated pepper (Capsicum) and its use in gene presence-absence variation analyses. New Phytologist, 220, 360\u2013363. https:\/\/doi.org\/10.1111\/nph.15413","journal-title":"New Phytologist"},{"key":"1604_CR102","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1038\/s41477-021-00928-8","volume":"7","author":"Z He","year":"2021","unstructured":"He, Z., Ji, R., Havlickova, L., Wang, L., Li, Y., Lee, H. T., Song, J., Koh, C., Yang, J., Zhang, M., Parkin, I. A. P., Wang, X., Edwards, D., King, G. J., Zou, J., Liu, K., Snowdon, R. J., Banga, S. S., Machackova, I., & Bancroft, I. (2021). Genome structural evolution in Brassica crops. Nature Plants, 7, 757\u2013765. https:\/\/doi.org\/10.1038\/s41477-021-00928-8","journal-title":"Nature Plants"},{"key":"1604_CR103","doi-asserted-by":"publisher","first-page":"1232","DOI":"10.1038\/s41588-023-01423-w","volume":"55","author":"Q He","year":"2023","unstructured":"He, Q., Tang, S., Zhi, H., Chen, J., Zhang, J., Liang, H., Alam, O., Li, H., Zhang, H., Xing, L., Li, X., Zhang, W., Wang, H., Shi, J., Du, H., Wu, H., Wang, L., Yang, P., Xing, L., & Diao, X. (2023). A graph-based genome and pan-genome variation of the model plant Setaria. Nature Genetics, 55, 1232\u20131242. https:\/\/doi.org\/10.1038\/s41588-023-01423-w","journal-title":"Nature Genetics"},{"key":"1604_CR104","doi-asserted-by":"publisher","first-page":"5377","DOI":"10.1038\/s41467-024-49679-y","volume":"15","author":"T H\u00e4m\u00e4l\u00e4","year":"2024","unstructured":"H\u00e4m\u00e4l\u00e4, T., Moore, C., Cowan, L., Carlile, M., Gopaulchan, D., Brandrud, M. K., Birkeland, S., Loose, M., Kol\u00e1\u0159, F., Koch, M. A., & Yant, L. (2024). Impact of whole-genome duplications on structural variant evolution in Cochlearia. Nature Communications, 15, 5377. https:\/\/doi.org\/10.1038\/s41467-024-49679-y","journal-title":"Nature Communications"},{"key":"1604_CR105","doi-asserted-by":"publisher","first-page":"3345","DOI":"10.1111\/pbi.70553","volume":"24","author":"G Droc","year":"2026","unstructured":"Droc, G., Giraud, D., Belser, C., Labadie, K., Duprat, S., Cruaud, C., Istace, B., Menezes, F. D. S., de Andrade Silva, E. M., Curk, F., Costantino, G., Soriano, A., Mournet, P., Dereeper, A., Miranda, M., Marchi, E., Santoni, S., Santana Silva, R. J., Sidibe-Bocs, S., & Ollitrault, P. (2026). A super-pangenome for cultivated citrus reveals evolutive features during the allopatric phase of their reticulate evolution. Plant Biotechnology Journal, 24, 3345\u20133367. https:\/\/doi.org\/10.1111\/pbi.70553","journal-title":"Plant Biotechnology Journal"},{"key":"1604_CR106","doi-asserted-by":"publisher","first-page":"9.9.1","DOI":"10.1002\/0471250953.bi0909s17","volume":"17","author":"MJ Donlin","year":"2007","unstructured":"Donlin, M. J. (2007). Using the generic genome browser (GBrowse). Current Protocols in Bioinformatics, 17, 9.9.1-9.9.24. https:\/\/doi.org\/10.1002\/0471250953.bi0909s17","journal-title":"Current Protocols in Bioinformatics"},{"key":"1604_CR107","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1093\/bib\/bbt001","volume":"14","author":"LD Stein","year":"2013","unstructured":"Stein, L. D. (2013). Using GBrowse 2.0 to visualize and share next-generation sequence data. Briefings in Bioinformatics, 14, 162\u2013171. https:\/\/doi.org\/10.1093\/bib\/bbt001","journal-title":"Briefings in Bioinformatics"},{"key":"1604_CR108","doi-asserted-by":"publisher","first-page":"1836","DOI":"10.1093\/bioinformatics\/btp314","volume":"25","author":"E Lee","year":"2009","unstructured":"Lee, E., Harris, N., Gibson, M., Chetty, R., & Lewis, S. (2009). Apollo: A community resource for genome annotation editing. Bioinformatics, 25, 1836\u20131837. https:\/\/doi.org\/10.1093\/bioinformatics\/btp314","journal-title":"Bioinformatics"},{"key":"1604_CR109","doi-asserted-by":"publisher","first-page":"3350","DOI":"10.1093\/bioinformatics\/btv383","volume":"31","author":"RR Wick","year":"2015","unstructured":"Wick, R. R., Schultz, M. B., Zobel, J., & Holt, K. E. (2015). Bandage: Interactive visualization of de novo genome assemblies. Bioinformatics, 31, 3350\u20133352. https:\/\/doi.org\/10.1093\/bioinformatics\/btv383","journal-title":"Bioinformatics"},{"key":"1604_CR110","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0924-1","volume":"17","author":"R Buels","year":"2016","unstructured":"Buels, R., Yao, E., Diesh, C. M., Hayes, R. D., Munoz-Torres, M., Helt, G., Goodstein, D. M., Elsik, C. G., Lewis, S. E., Stein, L., & Holmes, I. H. (2016). JBrowse: A dynamic web platform for genome visualization and analysis. Genome Biology, 17, Article 66. https:\/\/doi.org\/10.1186\/s13059-016-0924-1","journal-title":"Genome Biology"},{"key":"1604_CR111","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1038\/nbt.4227","volume":"36","author":"E Garrison","year":"2018","unstructured":"Garrison, E., Sir\u00e9n, J., Novak, A. M., Hickey, G., Eizenga, J. M., Dawson, E. T., Jones, W., Garg, S., Markello, C., Lin, M. F., Paten, B., & Durbin, R. (2018). Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nature Biotechnology, 36, 875\u2013879. https:\/\/doi.org\/10.1038\/nbt.4227","journal-title":"Nature Biotechnology"},{"key":"1604_CR112","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx977","volume":"46","author":"W Ding","year":"2018","unstructured":"Ding, W., Baumdicker, F., & Neher, R. A. (2018). PanX: Pan-genome analysis and exploration. Nucleic Acids Research, 46, Article e5. https:\/\/doi.org\/10.1093\/nar\/gkx977","journal-title":"Nucleic Acids Research"},{"key":"1604_CR113","doi-asserted-by":"publisher","first-page":"2853","DOI":"10.1093\/bioinformatics\/bty1046","volume":"35","author":"G Gonnella","year":"2019","unstructured":"Gonnella, G., Niehus, N., & Kurtz, S. (2019). GfaViz: Flexible and interactive visualization of GFA sequence graphs. Bioinformatics, 35, 2853\u20132855. https:\/\/doi.org\/10.1093\/bioinformatics\/bty1046","journal-title":"Bioinformatics"},{"key":"1604_CR114","doi-asserted-by":"publisher","first-page":"5318","DOI":"10.1093\/bioinformatics\/btz597","volume":"35","author":"W Beyer","year":"2019","unstructured":"Beyer, W., Novak, A. M., Hickey, G., Chan, J., Tan, V., Paten, B., & Zerbino, D. R. (2019). Sequence tube maps: Making graph genomes intuitive to commuters. Bioinformatics, 35, 5318\u20135320. https:\/\/doi.org\/10.1093\/bioinformatics\/btz597","journal-title":"Bioinformatics"},{"key":"1604_CR115","doi-asserted-by":"publisher","first-page":"4556","DOI":"10.1093\/bioinformatics\/btab688","volume":"37","author":"\u00c9 Durant","year":"2021","unstructured":"Durant, \u00c9., Sabot, F., Conte, M., & Rouard, M. (2021). Panache: A web browser-based viewer for linearized pangenomes. Bioinformatics, 37, 4556\u20134558. https:\/\/doi.org\/10.1093\/bioinformatics\/btab688","journal-title":"Bioinformatics"},{"key":"1604_CR116","doi-asserted-by":"publisher","first-page":"3319","DOI":"10.1093\/bioinformatics\/btac308","volume":"38","author":"A Guarracino","year":"2022","unstructured":"Guarracino, A., Heumos, S., Nahnsen, S., Prins, P., & Garrison, E. (2022). ODGI: Understanding pangenome graphs. Bioinformatics, 38, 3319\u20133326. https:\/\/doi.org\/10.1093\/bioinformatics\/btac308","journal-title":"Bioinformatics"},{"key":"1604_CR117","doi-asserted-by":"publisher","unstructured":"Li, F., Hu, H., Xiao, Z., Wang, J., Liu, J., Zhao, D., Fu, Y., Wang, Y., Yuan, X., Bu, S., Zhou, X., Zhao, J., & Wang, S. (2023). Visualization and review of reads alignment on the graphical pan-genome with VAG. https:\/\/doi.org\/10.1101\/2023.01.20.524849.","DOI":"10.1101\/2023.01.20.524849"},{"key":"1604_CR118","doi-asserted-by":"publisher","DOI":"10.1016\/j.ncrops.2026.100109","author":"Y Zhuang","year":"2026","unstructured":"Zhuang, Y., Li, X., Liu, L., Xu, R., & Zhang, D. (2026). Harnessing super pan-genomics for accelerated crop improvement. New Crops. https:\/\/doi.org\/10.1016\/j.ncrops.2026.100109","journal-title":"New Crops"},{"key":"1604_CR119","doi-asserted-by":"publisher","first-page":"D843","DOI":"10.1093\/nar\/gkp798","volume":"38","author":"D Grant","year":"2010","unstructured":"Grant, D., Nelson, R. T., Cannon, S. B., & Shoemaker, R. C. (2010). SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Research, 38, D843\u2013D846. https:\/\/doi.org\/10.1093\/nar\/gkp798","journal-title":"Nucleic Acids Research"},{"key":"1604_CR120","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1093\/nar\/gkw958","volume":"45","author":"C Sun","year":"2017","unstructured":"Sun, C., Hu, Z., Zheng, T., Lu, K., Zhao, Y., Wang, W., Shi, J., Wang, C., Lu, J., Zhang, D., Li, Z., & Wei, C. (2017). RPAN: Rice pan-genome browser for \u223c3000 rice genomes. Nucleic Acids Research, 45, 597\u2013605. https:\/\/doi.org\/10.1093\/nar\/gkw958","journal-title":"Nucleic Acids Research"},{"key":"1604_CR121","doi-asserted-by":"publisher","first-page":"D393","DOI":"10.1093\/nar\/gkh011","volume":"32","author":"CJ Lawrence","year":"2004","unstructured":"Lawrence, C. J., Dong, Q., Polacco, M. L., Seigfried, T. E., & Brendel, V. (2004). MaizeGDB, the community database for maize genetics and genomics. Nucleic Acids Research, 32, D393-397. https:\/\/doi.org\/10.1093\/nar\/gkh011","journal-title":"Nucleic Acids Research"},{"key":"1604_CR122","doi-asserted-by":"publisher","first-page":"D1146","DOI":"10.1093\/nar\/gky1046","volume":"47","author":"JL Portwood","year":"2019","unstructured":"Portwood, J. L., Woodhouse, M. R., Cannon, E. K., Gardiner, J. M., Harper, L. C., Schaeffer, M. L., Walsh, J. R., Sen, T. Z., Cho, K. T., Schott, D. A., Braun, B. L., Dietze, M., Dunfee, B., Elsik, C. G., Manchanda, N., Coe, E., Sachs, M., Stinard, P., Tolbert, J., \u2026 Andorf, C. M. (2019). MaizeGDB 2018: The maize multi-genome genetics and genomics database. Nucleic Acids Research, 47, D1146\u2013D1154. https:\/\/doi.org\/10.1093\/nar\/gky1046","journal-title":"Nucleic Acids Research"},{"key":"1604_CR123","doi-asserted-by":"publisher","first-page":"571","DOI":"10.1111\/tpj.14341","volume":"99","author":"T Lee","year":"2019","unstructured":"Lee, T., Lee, S., Yang, S., & Lee, I. (2019). MaizeNet: A co-functional network for network-assisted systems genetics in Zea mays. The Plant Journal, 99, 571\u2013582. https:\/\/doi.org\/10.1111\/tpj.14341","journal-title":"The Plant Journal"},{"key":"1604_CR124","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2020.101241","volume":"23","author":"S Gui","year":"2020","unstructured":"Gui, S., Yang, L., Li, J., Luo, J., Xu, X., Yuan, J., Chen, L., Li, W., Yang, X., Wu, S., Li, S., Wang, Y., Zhu, Y., Gao, Q., Yang, N., & Yan, J. (2020). ZEAMAP, a comprehensive database adapted to the maize multi-omics era. iScience, 23, Article 101241. https:\/\/doi.org\/10.1016\/j.isci.2020.101241","journal-title":"iScience"},{"key":"1604_CR125","doi-asserted-by":"publisher","first-page":"1965","DOI":"10.1016\/j.molp.2021.10.006","volume":"14","author":"S Ma","year":"2021","unstructured":"Ma, S., Wang, M., Wu, J., Guo, W., Chen, Y., Li, G., Wang, Y., Shi, W., Xia, G., Fu, D., Kang, Z., & Ni, F. (2021). WheatOmics: A platform combining multiple omics data to accelerate functional genomics studies in wheat. Molecular Plant, 14, 1965\u20131968. https:\/\/doi.org\/10.1016\/j.molp.2021.10.006","journal-title":"Molecular Plant"},{"key":"1604_CR126","doi-asserted-by":"publisher","first-page":"D1156","DOI":"10.1093\/nar\/gkq991","volume":"39","author":"Z Fei","year":"2011","unstructured":"Fei, Z., Joung, J.-G., Tang, X., Zheng, Y., Huang, M., Lee, J. M., McQuinn, R., Tieman, D. M., Alba, R., Klee, H. J., & Giovannoni, J. J. (2011). Tomato functional genomics database: A comprehensive resource and analysis package for tomato functional genomics. Nucleic Acids Research, 39, D1156\u2013D1163. https:\/\/doi.org\/10.1093\/nar\/gkq991","journal-title":"Nucleic Acids Research"},{"key":"1604_CR127","doi-asserted-by":"publisher","DOI":"10.1016\/j.ncrops.2023.10.001","volume":"1","author":"Y Cao","year":"2024","unstructured":"Cao, Y., She, J., Li, Z., Liu, Y., Tian, T., You, Q., Yan, H., Ma, X., Xu, W., & Su, Z. (2024). TomAP: A multi-omics data analysis platform for advancing functional genomics research in tomatoes. New Crops, 1, Article 100002. https:\/\/doi.org\/10.1016\/j.ncrops.2023.10.001","journal-title":"New Crops"},{"key":"1604_CR128","doi-asserted-by":"publisher","first-page":"baac080","DOI":"10.1093\/database\/baac080","volume":"2022","author":"F Dai","year":"2022","unstructured":"Dai, F., Chen, J., Zhang, Z., Liu, F., Li, J., Zhao, T., Hu, Y., Zhang, T., & Fang, L. (2022). COTTONOMICS: A comprehensive cotton multi-omics database. Database, 2022, baac080. https:\/\/doi.org\/10.1093\/database\/baac080","journal-title":"Database"},{"key":"1604_CR129","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-022-03846-9","volume":"22","author":"T Li","year":"2022","unstructured":"Li, T., Bian, J., Tang, M., Shangguan, H., Zeng, Y., Luo, R., Sun, H., Ke, Q., Nie, X., Li, Y., & Cui, L. (2022). BGFD: An integrated multi-omics database of barley gene families. BMC Plant Biology, 22, Article 454. https:\/\/doi.org\/10.1186\/s12870-022-03846-9","journal-title":"BMC Plant Biology"},{"key":"1604_CR130","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1111\/nph.15413","volume":"220","author":"L Ou","year":"2018","unstructured":"Ou, L., Li, D., Lv, J., Chen, W., Zhang, Z., Li, X., Yang, B., Zhou, S., Yang, S., Li, W., Gao, H., Zeng, Q., Yu, H., Ouyang, B., Li, F., Liu, F., Zheng, J., Liu, Y., Wang, J., \u2026 Zou, X. (2018). Pan-genome of cultivated pepper (Capsicum) and its use in gene presence\u2013absence variation analyses. The New Phytologist, 220, 360\u2013363.","journal-title":"The New Phytologist"},{"key":"1604_CR131","doi-asserted-by":"publisher","first-page":"2184","DOI":"10.1038\/s41467-017-02292-8","volume":"8","author":"SP Gordon","year":"2017","unstructured":"Gordon, S. P., Contreras-Moreira, B., Woods, D. P., Des Marais, D. L., Burgess, D., Shu, S., Stritt, C., Roulin, A. C., Schackwitz, W., Tyler, L., Martin, J., Lipzen, A., Dochy, N., Phillips, J., Barry, K., Geuten, K., Budak, H., Juenger, T. E., Amasino, R., & Vogel, J. P. (2017). Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nature Communication, 8, 2184. https:\/\/doi.org\/10.1038\/s41467-017-02292-8","journal-title":"Nature Communication"},{"key":"1604_CR132","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1111\/pbi.13491","volume":"19","author":"J Song","year":"2020","unstructured":"Song, J., Liu, D., Xie, W., Yang, Z., Guo, L., Liu, K., Yang, Q., & Chen, L. (2020). BnPIR: Brassica napus pan\u2010genome information resource for 1689 accessions. Plant Biotechnology Journal, 19, 412\u2013414. https:\/\/doi.org\/10.1111\/pbi.13491","journal-title":"Plant Biotechnology Journal"},{"key":"1604_CR133","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1016\/j.molp.2023.03.007","volume":"16","author":"Z Yang","year":"2023","unstructured":"Yang, Z., Wang, S., Wei, L., Huang, Y., Liu, D., Jia, Y., Luo, C., Lin, Y., Liang, C., Hu, Y., Dai, C., Guo, L., Zhou, Y., & Yang, Q.-Y. (2023). BnIR: A multi-omics database with various tools for Brassica napus research and breeding. Molecular Plant, 16, 775\u2013789. https:\/\/doi.org\/10.1016\/j.molp.2023.03.007","journal-title":"Molecular Plant"},{"key":"1604_CR134","doi-asserted-by":"publisher","first-page":"D1452","DOI":"10.1093\/nar\/gkaa979","volume":"49","author":"MK Tello-Ruiz","year":"2020","unstructured":"Tello-Ruiz, M. K., Naithani, S., Gupta, P., Olson, A., Wei, S., Preece, J., Jiao, Y., Wang, B., Chougule, K., Garg, P., Elser, J., Kumari, S., Kumar, V., Contreras-Moreira, B., Naamati, G., George, N., Cook, J., Bolser, D., D\u2019Eustachio, P., & Ware, D. (2020). Gramene 2021: Harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research, 49, D1452\u2013D1463. https:\/\/doi.org\/10.1093\/nar\/gkaa979","journal-title":"Nucleic Acids Research"},{"key":"1604_CR135","doi-asserted-by":"publisher","first-page":"D1464","DOI":"10.1093\/nar\/gkaa1068","volume":"49","author":"G Valentin","year":"2020","unstructured":"Valentin, G., Abdel, T., Ga\u00ebtan, D., Jean-Fran\u00e7ois, D., Matthieu, C., & Mathieu, R. (2020). GreenPhylDB v5: A comparative pangenomic database for plant genomes. Nucleic Acids Research, 49, D1464\u2013D1471. https:\/\/doi.org\/10.1093\/nar\/gkaa1068","journal-title":"Nucleic Acids Research"},{"key":"1604_CR136","doi-asserted-by":"publisher","DOI":"10.1016\/j.xplc.2024.100855","author":"B He","year":"2024","unstructured":"He, B., Bu, M., Lin, Q., Fu, Z., Xie, J., Fan, W., Li, J., Li, R., Hua, W., Liu, W., & Cui, P. (2024). CLAIR: An integrated lipid database across multiple crop species. Plant Communications. https:\/\/doi.org\/10.1016\/j.xplc.2024.100855","journal-title":"Plant Communications"},{"key":"1604_CR137","doi-asserted-by":"publisher","first-page":"D1588","DOI":"10.1093\/nar\/gkad963","volume":"52","author":"S Yang","year":"2023","unstructured":"Yang, S., Zong, W., Shi, L., Li, R., Ma, Z., Ma, S., Si, J., Wu, Z., Zhai, J., Ma, Y., Fan, Z., Chen, S., Huang, H., Zhang, D., Bao, Y., Li, R., & Xie, J. (2023). PPGR: A comprehensive perennial plant genomes and regulation database. Nucleic Acids Research, 52, D1588\u2013D1596. https:\/\/doi.org\/10.1093\/nar\/gkad963","journal-title":"Nucleic Acids Research"},{"key":"1604_CR138","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.70144","volume":"122","author":"M Jiang","year":"2025","unstructured":"Jiang, M., Qian, Q., Lu, M., Chen, M., Fan, Z., Shang, Y., Bu, C., Du, Z., Song, S., Zeng, J., & Xiao, J. (2025). PlantPan: A comprehensive multi-species plant pan-genome database. The Plant Journal, 122, Article e70144. https:\/\/doi.org\/10.1111\/tpj.70144","journal-title":"The Plant Journal"},{"key":"1604_CR139","doi-asserted-by":"publisher","first-page":"D1563","DOI":"10.1093\/nar\/gkae833","volume":"53","author":"D Liu","year":"2024","unstructured":"Liu, D., Luo, C., Dai, R., Huang, X., Chen, X., He, L., Mao, H., Li, J., Zhang, L., Yang, Q.-Y., & Mei, Z. (2024). AMIR: A multi-omics data platform for Asteraceae plants genetics and breeding research. Nucleic Acids Research, 53, D1563\u2013D1575. https:\/\/doi.org\/10.1093\/nar\/gkae833","journal-title":"Nucleic Acids Research"},{"key":"1604_CR140","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-51854-0","volume":"15","author":"H He","year":"2024","unstructured":"He, H., Leng, Y., Cao, X., Zhu, Y., Li, X., Yuan, Q., Zhang, B., He, W., Wei, H., Liu, X., Xu, Q., Guo, M., Zhang, H., Yang, L., Lv, Y., Wang, X., Shi, C., Zhang, Z., Chen, W., & Shang, L. (2024). The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice. Nature Communications, 15, Article 7291. https:\/\/doi.org\/10.1038\/s41467-024-51854-0","journal-title":"Nature Communications"},{"key":"1604_CR141","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1016\/j.jgg.2025.03.005","volume":"52","author":"X Tan","year":"2025","unstructured":"Tan, X., Zeng, W., Yang, Y., Lin, Z., Li, F., Liu, J., Chen, S., Liu, Y.-G., Xie, W., & Xie, X. (2025). Genome-wide profiling of polymorphic short tandem repeats and their influence on gene expression and trait variation in diverse rice populations. Journal of Genetics and Genomics, 52, 733\u2013746. https:\/\/doi.org\/10.1016\/j.jgg.2025.03.005","journal-title":"Journal of Genetics and Genomics"},{"key":"1604_CR142","doi-asserted-by":"publisher","first-page":"1567","DOI":"10.1038\/s41467-023-37004-y","volume":"14","author":"Y Zhou","year":"2023","unstructured":"Zhou, Y., Yu, Z., Chebotarov, D., Chougule, K., Lu, Z., Rivera, L. F., Kathiresan, N., Al-Bader, N., Mohammed, N., Alsantely, A., Mussurova, S., Santos, J., Thimma, M., Troukhan, M., Fornasiero, A., Green, C. D., Copetti, D., Kudrna, D., Llaca, V., & Wing, R. A. (2023). Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice. Nature Communications, 14, 1567. https:\/\/doi.org\/10.1038\/s41467-023-37004-y","journal-title":"Nature Communications"},{"key":"1604_CR143","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1016\/j.scib.2023.12.048","volume":"69","author":"W He","year":"2024","unstructured":"He, W., He, H., Yuan, Q., Zhang, H., Li, X., Wang, T., Yang, Y., Yang, L., Yang, Y., Liu, X., Wei, H., Zhang, H., Zhang, B., Guo, M., Leng, Y., Shi, C., Lv, Y., Chen, W., Wang, X., & Shang, L. (2024). Widespread inversions shape the genetic and phenotypic diversity in rice. Science Bulletin, 69, 593\u2013596. https:\/\/doi.org\/10.1016\/j.scib.2023.12.048","journal-title":"Science Bulletin"},{"key":"1604_CR144","doi-asserted-by":"publisher","unstructured":"Romain, S., Dubois, S., Legeai, F., & Lemaitre, C. (2025). Investigating the topological motifs of inversions in pangenome graphs. https:\/\/doi.org\/10.1101\/2025.03.14.643331.","DOI":"10.1101\/2025.03.14.643331"},{"key":"1604_CR145","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1111\/jipb.13607","volume":"66","author":"Y Lv","year":"2024","unstructured":"Lv, Y., Liu, C., Li, X., Wang, Y., He, H., He, W., Chen, W., Yang, L., Dai, X., Cao, X., Yu, X., Liu, J., Zhang, B., Wei, H., Zhang, H., Qian, H., Shi, C., Leng, Y., Liu, X., & Shang, L. (2024). A centromere map based on super pan-genome highlights the structure and function of rice centromeres. Journal of Integrative Plant Biology, 66, 196\u2013207. https:\/\/doi.org\/10.1111\/jipb.13607","journal-title":"Journal of Integrative Plant Biology"},{"key":"1604_CR146","doi-asserted-by":"publisher","first-page":"4372","DOI":"10.1093\/plcell\/koae181","volume":"36","author":"H Zhang","year":"2024","unstructured":"Zhang, H., Chen, W., Zhu, D., Zhang, B., Xu, Q., Shi, C., He, H., Dai, X., Li, Y., He, W., Lv, Y., Yang, L., Cao, X., Cui, Y., Leng, Y., Wei, H., Liu, X., Zhang, B., Wang, X., & Shang, L. (2024). Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice. The Plant Cell, 36, 4372\u20134387. https:\/\/doi.org\/10.1093\/plcell\/koae181","journal-title":"The Plant Cell"},{"key":"1604_CR147","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2021.563953","volume":"12","author":"Y Yang","year":"2021","unstructured":"Yang, Y., Saand, M. A., Huang, L., Abdelaal, W. B., Zhang, J., Wu, Y., Li, J., Sirohi, M. H., & Wang, F. (2021). Applications of multi-omics technologies for crop improvement. Frontiers in Plant Science, 12, Article 563953. https:\/\/doi.org\/10.3389\/fpls.2021.563953","journal-title":"Frontiers in Plant Science"},{"key":"1604_CR148","doi-asserted-by":"publisher","first-page":"nwae043","DOI":"10.1093\/nsr\/nwae043","volume":"11","author":"H Wei","year":"2024","unstructured":"Wei, H., Wang, X., Zhang, Z., Yang, L., Zhang, Q., Li, Y., He, H., Chen, D., Zhang, B., Zheng, C., Leng, Y., Cao, X., Cui, Y., Shi, C., Liu, Y., Lv, Y., Ma, J., He, W., Liu, X., & Shang, L. (2024). Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice. National Science Review, 11, nwae043.","journal-title":"National Science Review"},{"key":"1604_CR149","doi-asserted-by":"publisher","DOI":"10.1016\/j.xplc.2024.100813","author":"\u00c1 Ferrero-Serrano","year":"2024","unstructured":"Ferrero-Serrano, \u00c1., Chakravorty, D., Kirven, K. J., & Assmann, S. M. (2024). Oryza CLIMtools: A genome\u2013environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits. Plant Communications. https:\/\/doi.org\/10.1016\/j.xplc.2024.100813","journal-title":"Plant Communications"},{"key":"1604_CR150","doi-asserted-by":"publisher","first-page":"1363","DOI":"10.1016\/j.molp.2023.08.005","volume":"16","author":"A Raza","year":"2023","unstructured":"Raza, A., Bohra, A., Garg, V., & Varshney, R. K. (2023). Back to wild relatives for future breeding through super-pangenome. Molecular Plant, 16, 1363\u20131365. https:\/\/doi.org\/10.1016\/j.molp.2023.08.005","journal-title":"Molecular Plant"},{"key":"1604_CR151","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1146\/annurev-arplant-080720-090632","volume":"72","author":"Y Liang","year":"2021","unstructured":"Liang, Y., Liu, H.-J., Yan, J., & Tian, F. (2021). Natural variation in crops: Realized understanding, continuing promise. Annual Review of Plant Biology, 72, 357\u2013385. https:\/\/doi.org\/10.1146\/annurev-arplant-080720-090632","journal-title":"Annual Review of Plant Biology"},{"key":"1604_CR152","doi-asserted-by":"publisher","first-page":"2313","DOI":"10.1016\/j.cell.2023.04.008","volume":"186","author":"Y Wu","year":"2023","unstructured":"Wu, Y., Li, D., Hu, Y., Li, H., Ramstein, G. P., Zhou, S., Zhang, X., Bao, Z., Zhang, Y., Song, B., Zhou, Y., Zhou, Y., Gagnon, E., S\u00e4rkinen, T., Knapp, S., Zhang, C., St\u00e4dler, T., Buckler, E. S., & Huang, S. (2023). Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell, 186, 2313-2328.e15. https:\/\/doi.org\/10.1016\/j.cell.2023.04.008","journal-title":"Cell"},{"key":"1604_CR153","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1038\/s41588-020-00769-9","volume":"53","author":"X Wei","year":"2021","unstructured":"Wei, X., Qiu, J., Yong, K., Fan, J., Zhang, Q., Hua, H., Liu, J., Wang, Q., Olsen, K. M., Han, B., & Huang, X. (2021). A quantitative genomics map of rice provides genetic insights and guides breeding. Nature Genetics, 53, 243\u2013253. https:\/\/doi.org\/10.1038\/s41588-020-00769-9","journal-title":"Nature Genetics"},{"key":"1604_CR154","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.molp.2020.12.006","volume":"14","author":"Q Chen","year":"2021","unstructured":"Chen, Q., Li, W., Tan, L., & Tian, F. (2021). Harnessing knowledge from maize and rice domestication for new crop breeding. Molecular Plant, 14, 9\u201326. https:\/\/doi.org\/10.1016\/j.molp.2020.12.006","journal-title":"Molecular Plant"},{"key":"1604_CR155","doi-asserted-by":"publisher","first-page":"2828","DOI":"10.1016\/j.cell.2022.04.036","volume":"185","author":"X Huang","year":"2022","unstructured":"Huang, X., Huang, S., Han, B., & Li, J. (2022). The integrated genomics of crop domestication and breeding. Cell, 185, 2828\u20132839. https:\/\/doi.org\/10.1016\/j.cell.2022.04.036","journal-title":"Cell"},{"key":"1604_CR156","doi-asserted-by":"publisher","first-page":"1156","DOI":"10.1016\/j.cell.2021.01.013","volume":"184","author":"H Yu","year":"2021","unstructured":"Yu, H., Lin, T., Meng, X., Du, H., Zhang, J., Liu, G., Chen, M., Jing, Y., Kou, L., Li, X., Gao, Q., Liang, Y., Liu, X., Fan, Z., Liang, Y., Cheng, Z., Chen, M., Tian, Z., Wang, Y., & Li, J. (2021). A route to de novo domestication of wild allotetraploid rice. Cell, 184, 1156-1170.e14. https:\/\/doi.org\/10.1016\/j.cell.2021.01.013","journal-title":"Cell"},{"key":"1604_CR157","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1007\/978-981-95-5109-5_3","volume-title":"DNA of sustainability: Genomic insights into food security challenges","author":"AW Khan","year":"2026","unstructured":"Khan, A. W., Gupta, S., & Nguyen, H. T. (2026). Pangenomes, super-pangenomes and beyond. In V. Garg, R. Henry, & R. K. Varshney (Eds.), DNA of sustainability: Genomic insights into food security challenges (pp. 33\u201360). Springer Nature. https:\/\/doi.org\/10.1007\/978-981-95-5109-5_3"},{"key":"1604_CR158","doi-asserted-by":"publisher","first-page":"3679","DOI":"10.1111\/pbi.70591","volume":"24","author":"S Nie","year":"2026","unstructured":"Nie, S., Li, F., Li, R., Wang, J., Ma, Y., Chan, C. K. K., Zhao, J., & Hu, H. (2026). Challenges in bringing pangenome research into breeding: A case study in rice. Plant Biotechnology Journal, 24, 3679\u20133690. https:\/\/doi.org\/10.1111\/pbi.70591","journal-title":"Plant Biotechnology Journal"},{"key":"1604_CR159","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2026.1793924","volume":"17","author":"S Diakite","year":"2026","unstructured":"Diakite, S., Norman, P. E., Kamara, L., Pehlivan, N., & Zargar, M. (2026). Genetic enhancement of root, tuber and cereal crops via pangenomics, multi-omics integration and AI-driven prediction. Frontiers in Plant Science, 17, Article 1793924. https:\/\/doi.org\/10.3389\/fpls.2026.1793924","journal-title":"Frontiers in Plant Science"},{"key":"1604_CR160","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2025.101067","volume":"6","author":"V Loegler","year":"2026","unstructured":"Loegler, V., Friedrich, A., & Schacherer, J. (2026). Dynamics of genome evolution in the era of pangenome analysis. Cell Genomics, 6, Article 101067. https:\/\/doi.org\/10.1016\/j.xgen.2025.101067","journal-title":"Cell Genomics"},{"key":"1604_CR161","doi-asserted-by":"publisher","DOI":"10.1186\/s12284-026-00893-w","volume":"19","author":"H Tao","year":"2026","unstructured":"Tao, H., Wu, S., Wu, G., Chen, X., Sun, Y., Zhu, X., Chen, L., Feng, C., Kabore, M. A. F., Woldegiorgis, S. T., Zhang, L., Ai, Y., Liu, W., & He, H. (2026). Pan-genome of wild and cultivated rice uncovers genetic diversity, lost and selected sequences during rice domestication. Rice, 19, Article 21. https:\/\/doi.org\/10.1186\/s12284-026-00893-w","journal-title":"Rice"},{"key":"1604_CR162","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2025.1673637","volume":"16","author":"C Liu","year":"2025","unstructured":"Liu, C., Xu, H., Li, Z., Wang, Y., Zhang, J., Qiao, S., & Zhang, H. (2025). From map to blueprint: The plant pan-genome unraveling genetic mysteries and powering precision breeding. Frontiers in Plant Science, 16, Article 1673637. https:\/\/doi.org\/10.3389\/fpls.2025.1673637","journal-title":"Frontiers in Plant Science"},{"key":"1604_CR163","doi-asserted-by":"publisher","DOI":"10.3390\/ijms232113420","volume":"23","author":"A Hameed","year":"2022","unstructured":"Hameed, A., Poznanski, P., Nadolska-Orczyk, A., & Orczyk, W. (2022). Graph pangenomes track genetic variants for crop improvement. International Journal of Molecular Sciences, 23, Article 13420. https:\/\/doi.org\/10.3390\/ijms232113420","journal-title":"International Journal of Molecular Sciences"},{"key":"1604_CR164","doi-asserted-by":"publisher","first-page":"eadm8762","DOI":"10.1126\/science.adm8762","volume":"385","author":"X Wei","year":"2024","unstructured":"Wei, X., Chen, M., Zhang, Q., Gong, J., Liu, J., Yong, K., Wang, Q., Fan, J., Chen, S., Hua, H., Luo, Z., Zhao, X., Wang, X., Li, W., Cong, J., Yu, X., Wang, Z., Huang, R., Chen, J., & Huang, X. (2024). Genomic investigation of 18,421 lines reveals the genetic architecture of rice. Science, 385, eadm8762. https:\/\/doi.org\/10.1126\/science.adm8762","journal-title":"Science"},{"key":"1604_CR165","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1016\/j.gpb.2023.04.004","volume":"21","author":"W Kong","year":"2023","unstructured":"Kong, W., Wang, Y., Zhang, S., Yu, J., & Zhang, X. (2023). Recent advances in assembly of complex plant genomes. Genomics, Proteomics & Bioinformatics, 21, 427\u2013439. https:\/\/doi.org\/10.1016\/j.gpb.2023.04.004","journal-title":"Genomics, Proteomics & Bioinformatics"}],"container-title":["Molecular Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s12033-026-01604-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s12033-026-01604-y","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s12033-026-01604-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T08:36:34Z","timestamp":1787128594000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s12033-026-01604-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,19]]},"references-count":165,"alternative-id":["1604"],"URL":"https:\/\/doi.org\/10.1007\/s12033-026-01604-y","relation":{},"ISSN":["1073-6085","1559-0305"],"issn-type":[{"value":"1073-6085","type":"print"},{"value":"1559-0305","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,19]]},"assertion":[{"value":"16 January 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 August 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 August 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.","order":1,"name":"Ethics","label":"Conflict of interest","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Ethical Approval and Consent to Participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All the authors have read, finalized, and agreed with the final version of the manuscript for possible publication.","order":3,"name":"Ethics","label":"Consent to Publish","group":{"name":"EthicsHeading","label":"Declarations"}}]}}