{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T13:24:02Z","timestamp":1787059442869,"version":"build-2736575974"},"reference-count":246,"publisher":"MDPI AG","issue":"16","license":[{"start":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T00:00:00Z","timestamp":1787011200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32260089"],"award-info":[{"award-number":["32260089"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["32260089"],"award-info":[{"award-number":["32260089"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Science and Technology Department Foundation of Guizhou Province","award":["QKHJC-MS [2025]371"],"award-info":[{"award-number":["QKHJC-MS [2025]371"]}]},{"name":"Future Outstanding Teachers Training Program of Zunyi Medical University","award":["XJ2023-JX-01-06"],"award-info":[{"award-number":["XJ2023-JX-01-06"]}]},{"award":["XJ2023-JX-01-06"],"award-info":[{"award-number":["XJ2023-JX-01-06"]}],"id":[{"id":"https:\/\/ror.org\/00g5b0g93","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Inaugural Class Advisor Studios at Zunyi Medical University","award":["2024BZR-01"],"award-info":[{"award-number":["2024BZR-01"]}]},{"award":["2024BZR-01"],"award-info":[{"award-number":["2024BZR-01"]}],"id":[{"id":"https:\/\/ror.org\/00g5b0g93","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Joint Fund of Zunyi Bureau of Industry and Information Technology & Zunyi Medical University","award":["Zunshi Kehe HZ Zi (2026) No. 286"],"award-info":[{"award-number":["Zunshi Kehe HZ Zi (2026) No. 286"]}]},{"name":"Zunyi Science and Technology Innovation Team for Tissue Culture Technology of Chinese Medicinal Materials","award":["Zun KCT (2025) No. 87"],"award-info":[{"award-number":["Zun KCT (2025) No. 87"]}]},{"name":"Joint Fund of Zunyi Bureau of Industry and Information Technology & Zunyi Academy of Agricultural Sciences","award":["Zunshi Kehe HZ Zi (2026) No. 158"],"award-info":[{"award-number":["Zunshi Kehe HZ Zi (2026) No. 158"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Plant genomes exhibit extensive structural diversity generated by large-scale genomic alterations, collectively known as structural variations (SVs). Unlike single nucleotide polymorphisms (SNPs) and small insertions\/deletions (indels), SVs can reshape genome architecture through changes in sequence content, gene dosage, regulatory landscapes, and chromosome organization. Recent advances in long-read sequencing (LRS), pan-genome construction, and multi-omics technologies have greatly expanded our ability to identify and interpret SVs across plant species. In this review, we summarize recent progress in understanding the formation mechanisms, classification, and functional consequences of plant SVs. We discuss major sources of SV generation, including transposable element activity, non-allelic homologous recombination (NAHR), horizontal gene transfer (HGT), and genome restructuring following polyploidization. We further highlight how LRS and graph-based pan-genomes overcome limitations of traditional linear reference genomes and enable more comprehensive characterization of genetic diversity. Beyond variant discovery, we emphasize the importance of integrating genomic, transcriptomic, epigenomic, proteomic, metabolomic, and spatial omics datasets to decipher how SVs influence gene regulation and complex agronomic traits. We also discuss current challenges, including repetitive genomes, polyploidy, computational complexity, and translation of SV knowledge into practical breeding applications. Together, these advances establish SV-centered genomics as a critical framework for understanding plant genome evolution and accelerating precision crop improvement.<\/jats:p>","DOI":"10.3390\/plants15162498","type":"journal-article","created":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T12:09:32Z","timestamp":1787054972000},"page":"2498","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Structural Variation and Its Roles in Plant Genomes"],"prefix":"10.3390","volume":"15","author":[{"given":"Ruyi","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi 563099, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Letong","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi 563099, China"},{"name":"Key Laboratory of Cancer Prevention and Treatment of Guizhou Province, Zunyi 563000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingru","family":"Mu","sequence":"additional","affiliation":[{"name":"Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi 563099, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Lu","sequence":"additional","affiliation":[{"name":"Special Key Laboratory of Oral Disease Research and High Education Institute in Guizhou Province, School of Stomatology, Zunyi Medical University, Zunyi 563000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yifei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi 563099, China"},{"name":"Zunyi Academy of Agricultural Sciences, Zunyi 563099, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kuanping","family":"Deng","sequence":"additional","affiliation":[{"name":"Zunyi Academy of Agricultural Sciences, Zunyi 563099, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3695-2997","authenticated-orcid":false,"given":"Delin","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi 563099, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1146\/annurev-arplant-090823-015358","article-title":"What Are We Learning from Plant Pangenomes?","volume":"76","author":"Jayakodi","year":"2025","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.pbi.2019.12.005","article-title":"Plant pangenomics: Approaches, applications and advancements","volume":"54","author":"Danilevicz","year":"2020","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1093\/plcell\/koaa038","article-title":"Anno genominis XX: 20 years of Arabidopsis genomics","volume":"33","author":"Provart","year":"2021","journal-title":"Plant Cell"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"The Arabidopsis Genome Initiative (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796\u2013815.","DOI":"10.1038\/35048692"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2672221","DOI":"10.1080\/15592324.2026.2672221","article-title":"Metabolic reprogramming in plant defense: Linking signaling networks to metabolomics-driven insights","volume":"21","author":"Khan","year":"2026","journal-title":"Plant Signal. Behav."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"e2502160122","DOI":"10.1073\/pnas.2502160122","article-title":"Evaluating plant growth-defense trade-offs by modeling the interaction between primary and secondary metabolism","volume":"122","author":"Zrimec","year":"2025","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1252","DOI":"10.1016\/j.molp.2023.07.009","article-title":"Plant genome resequencing and population genomics: Current status and future prospects","volume":"16","author":"Song","year":"2023","journal-title":"Mol. Plant"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1186\/s13059-021-02488-8","article-title":"Genomic insight into balancing high yield, good quality, and blast resistance of japonica rice","volume":"22","author":"Xiao","year":"2021","journal-title":"Genome Biol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1016\/j.plaphy.2020.04.032","article-title":"OsABAR1, a novel GRAM domain-containing protein, confers drought and salt tolerance via an ABA-dependent pathway in rice","volume":"152","author":"Zheng","year":"2020","journal-title":"Plant Physiol. Biochem."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1093\/plcell\/koaa002","article-title":"Plant NLR diversity: The known unknowns of pan-NLRomes","volume":"33","author":"Barragan","year":"2021","journal-title":"Plant Cell"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"koaf109","DOI":"10.1093\/plcell\/koaf109","article-title":"The resistance awakens: Diversity at the DNA, RNA, and protein levels informs engineering of plant immune receptors from Arabidopsis to crops","volume":"37","author":"Sutherland","year":"2025","journal-title":"Plant Cell"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Pokrovac, I., and Pezer, \u017d. (2022). Recent advances and current challenges in population genomics of structural variation in animals and plants. Front. Genet., 13.","DOI":"10.3389\/fgene.2022.1060898"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Wang, X., Liu, C., Sun, X., Sun, G., Zong, C., Qi, Y., Bai, Y., Li, W., Kong, F., and Li, H. (2025). How Structural Variations Influence Crop Improvement. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26146635"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s13059-023-02854-8","article-title":"Pan-3D genome analysis reveals structural and functional differentiation of soybean genomes","volume":"24","author":"Ni","year":"2023","journal-title":"Genome Biol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"msag087","DOI":"10.1093\/molbev\/msag087","article-title":"From structural pangenomes to functional panomics in plants","volume":"43","author":"Cochetel","year":"2026","journal-title":"Mol. Biol. Evol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e21838","DOI":"10.1002\/advs.202521838","article-title":"Haplotype-Resolved 3D Genomic Landscapes and Their Impacts on Agronomic Traits in Grapevine","volume":"13","author":"Peng","year":"2026","journal-title":"Adv. Sci."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1016\/j.molp.2022.12.009","article-title":"Plant pan-genomics and its applications","volume":"16","author":"Shi","year":"2023","journal-title":"Mol. Plant"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.pbi.2015.01.008","article-title":"Patterns of genomic changes with crop domestication and breeding","volume":"24","author":"Shi","year":"2015","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2828","DOI":"10.1016\/j.cell.2022.04.036","article-title":"The integrated genomics of crop domestication and breeding","volume":"185","author":"Huang","year":"2022","journal-title":"Cell"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial \u201cpan-genome\u201d","volume":"102","author":"Tettelin","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1038\/s41576-020-0210-7","article-title":"Pan-genomics in the human genome era","volume":"21","author":"Sherman","year":"2020","journal-title":"Nat. Rev. Genet."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1038\/nbt.2979","article-title":"De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits","volume":"32","author":"Li","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1038\/s41586-026-10229-9","article-title":"A sorghum pangenome reference improves global crop trait discovery","volume":"652","author":"Morris","year":"2026","journal-title":"Nature"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1101\/gr.278396.123","article-title":"Major impacts of widespread structural variation on sorghum","volume":"34","author":"Zhang","year":"2024","journal-title":"Genome Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"e20068","DOI":"10.1002\/advs.202520068","article-title":"Pan-3D Genome Analysis Reveals the Roles of Structural Variation in Chicken Chromatin Architectures, Domestication and Production Traits","volume":"13","author":"Zhou","year":"2026","journal-title":"Adv. Sci."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"gkae1267","DOI":"10.1093\/nar\/gkae1267","article-title":"Uncovering topologically associating domains from three-dimensional genome maps with TADGATE","volume":"53","author":"Dang","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1016\/j.cell.2015.10.026","article-title":"Stable Chromosome Condensation Revealed by Chromosome Conformation Capture","volume":"163","author":"Eagen","year":"2015","journal-title":"Cell"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"eaaw1668","DOI":"10.1126\/sciadv.aaw1668","article-title":"Principles of genome folding into topologically associating domains","volume":"5","author":"Szabo","year":"2019","journal-title":"Sci. Adv."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1168","DOI":"10.1038\/s41559-026-03069-3","article-title":"Dynamic reorganization of three-dimensional genome architecture during Populus diversification","volume":"10","author":"Shi","year":"2026","journal-title":"Nat. Ecol. Evol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/j.tplants.2021.10.006","article-title":"Twenty years of plant genome sequencing: Achievements and challenges","volume":"27","author":"Sun","year":"2022","journal-title":"Trends Plant Sci."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"113","DOI":"10.3390\/applbiosci1020008","article-title":"Progress in Plant Genome Sequencing","volume":"1","author":"Henry","year":"2022","journal-title":"Appl. Biosci."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1016\/j.molp.2017.02.010","article-title":"Whole-Genome Sequencing and Analysis of the Chinese Herbal Plant Panax notoginseng","volume":"10","author":"Chen","year":"2017","journal-title":"Mol. Plant"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/j.apsb.2019.08.004","article-title":"Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans","volume":"10","author":"Liu","year":"2020","journal-title":"Acta Pharm. Sin. B"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2827","DOI":"10.1111\/jipb.70240","article-title":"TADs, CGVs, and compartmentalization in genomes: Providing a new way for crop domestication and improvement","volume":"68","author":"Zaman","year":"2026","journal-title":"J. Integr. Plant Biol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2153","DOI":"10.1111\/pbi.13646","article-title":"Current status of structural variation studies in plants","volume":"19","author":"Yuan","year":"2021","journal-title":"Plant Biotechnol. J."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s13059-020-02224-8","article-title":"How the pan-genome is changing crop genomics and improvement","volume":"22","author":"Qiu","year":"2021","journal-title":"Genome Biol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1186\/s13059-015-0633-1","article-title":"Detecting non-allelic homologous recombination from high-throughput sequencing data","volume":"16","author":"Parks","year":"2015","journal-title":"Genome Biol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1016\/j.molp.2022.02.001","article-title":"Major episodes of horizontal gene transfer drove the evolution of land plants","volume":"15","author":"Ma","year":"2022","journal-title":"Mol. Plant"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1038\/s41477-018-0136-7","article-title":"Gene retention, fractionation and subgenome differences in polyploid plants","volume":"4","author":"Cheng","year":"2018","journal-title":"Nat. Plants"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1073\/pnas.36.6.344","article-title":"The origin and behavior of mutable loci in maize","volume":"36","author":"McClintock","year":"1950","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/nrg3374","article-title":"How important are transposons for plant evolution?","volume":"14","author":"Lisch","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.cell.2020.05.021","article-title":"Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato","volume":"182","author":"Alonge","year":"2020","journal-title":"Cell"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/j.molp.2019.11.009","article-title":"Evolution and Domestication Footprints Uncovered from the Genomes of Coix","volume":"13","author":"Liu","year":"2020","journal-title":"Mol. Plant"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1016\/j.tig.2025.12.007","article-title":"The enigma of transposable element abundance: Lessons from Arabidopsis","volume":"42","author":"Yang","year":"2026","journal-title":"Trends Genet."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"11376","DOI":"10.1073\/pnas.0704145104","article-title":"Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize","volume":"104","author":"Salvi","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1038\/ng.942","article-title":"Identification of a functional transposon insertion in the maize domestication gene tb1","volume":"43","author":"Studer","year":"2011","journal-title":"Nat. Genet."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"16969","DOI":"10.1073\/pnas.1310949110","article-title":"CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize","volume":"110","author":"Yang","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"E334","DOI":"10.1073\/pnas.1718058115","article-title":"ZmCCT9 enhances maize adaptation to higher latitudes","volume":"115","author":"Huang","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"4865","DOI":"10.1038\/s41467-023-40407-6","article-title":"Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica","volume":"14","author":"Zhang","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1038\/s41467-020-15040-2","article-title":"Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy","volume":"11","author":"Li","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"5728","DOI":"10.1038\/s41467-024-49913-7","article-title":"Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen","volume":"15","author":"Tralamazza","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1038\/ng.2309","article-title":"Comparative population genomics of maize domestication and improvement","volume":"44","author":"Hufford","year":"2012","journal-title":"Nat. Genet."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"102886","DOI":"10.1016\/j.copbio.2022.102886","article-title":"Era of gapless plant genomes: Innovations in sequencing and mapping technologies revolutionize genomics and breeding","volume":"79","author":"Gladman","year":"2023","journal-title":"Curr. Opin. Biotechnol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Shivhare, R., and Lata, C. (2016). Exploration of Genetic and Genomic Resources for Abiotic and Biotic Stress Tolerance in Pearl Millet. Front. Plant Sci., 7.","DOI":"10.3389\/fpls.2016.02069"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/j.tig.2015.03.010","article-title":"Unraveling the 3D genome: Genomics tools for multiscale exploration","volume":"31","author":"Risca","year":"2015","journal-title":"Trends Genet."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1016\/j.jgg.2020.06.007","article-title":"Decoding the plant genome: From epigenome to 3D organization","volume":"47","author":"Ouyang","year":"2020","journal-title":"J. Genet. Genom."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Wang, J., Zhou, Q., Liu, Y., Li, R., Lan, L., Zhao, J., Yang, Z., Jia, Y., and Hu, H. (2025). Editorial: Exploring structural variants in plant pangenomics: Innovations and applications. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1700222"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1111\/jipb.70098","article-title":"Structural variation drives rhizome innovation and adaptive divergence in sister Medicago species","volume":"68","author":"Hu","year":"2026","journal-title":"J. Integr. Plant Biol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1093\/bfgp\/elv014","article-title":"A decade of structural variants: Description, history and methods to detect structural variation","volume":"14","author":"Docampo","year":"2015","journal-title":"Brief. Funct. Genom."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"87","DOI":"10.5808\/GI.2014.12.3.87","article-title":"Transposable elements and genome size variations in plants","volume":"12","author":"Lee","year":"2014","journal-title":"Genom. Inform."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Wang, J., Ren, M., Zhao, M., Du, H., Huang, S., Wang, S., Hou, R., Jiang, X., Yan, C., and Li, J. (2026). Mitochondrial genome assembly, comparative analysis of two caprifoliaceae species, and insights into adaptive evolution. BMC Plant Biol., 26.","DOI":"10.1186\/s12870-026-08519-5"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"107760","DOI":"10.1016\/j.ympev.2023.107760","article-title":"Rate accelerations in plastid and mitochondrial genomes of Cyperaceae occur in the same clades","volume":"182","author":"Lee","year":"2023","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Sheng, W., and Kuang, Q. (2026). Characterization of the mitochondrial genome of the aquatic vegetable Eleocharis dulcis (Burm. f.) Trin. ex Hensch.: The first representative of genus Eleocharis with evolutionary insights in Cyperaceae. BMC Plant Biol., 26.","DOI":"10.1186\/s12870-026-09085-6"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"e70216","DOI":"10.1111\/mec.70216","article-title":"A Beginner\u2019s Guide to Structural Variants in Eco-Evolutionary Population Genomics","volume":"35","author":"Stuart","year":"2026","journal-title":"Mol. Ecol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1038\/s41467-022-28362-0","article-title":"Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber","volume":"13","author":"Li","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Guo, N., Wang, S., Gao, L., Liu, Y., Wang, X., Lai, E., Duan, M., Wang, G., Li, J., and Yang, M. (2021). Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification. BMC Biol., 19.","DOI":"10.1186\/s12915-021-01031-2"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"e2102914118","DOI":"10.1073\/pnas.2102914118","article-title":"Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree","volume":"118","author":"Wafula","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"102818","DOI":"10.1016\/j.pbi.2025.102818","article-title":"The natural history of transposons in plant pangenomes and panepigenomes","volume":"88","author":"Quadrana","year":"2025","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Arvas, Y.E., Marakli, S., Kaya, Y., and Kalendar, R. (2023). The power of retrotransposons in high-throughput genotyping and sequencing. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1174339"},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Mhiri, C., Borges, F., and Grandbastien, M.A. (2022). Specificities and Dynamics of Transposable Elements in Land Plants. Biology, 11.","DOI":"10.3390\/biology11040488"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1038\/ng1615","article-title":"Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize","volume":"37","author":"Morgante","year":"2005","journal-title":"Nat. Genet."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41588-018-0182-0","article-title":"Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes","volume":"50","author":"Sun","year":"2018","journal-title":"Nat. Genet."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1038\/s41477-025-02002-z","article-title":"The regulatory potential of transposable elements in maize","volume":"11","author":"Bubb","year":"2025","journal-title":"Nat. Plants"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"100291","DOI":"10.1016\/j.xgen.2023.100291","article-title":"Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements","volume":"3","author":"Ferraj","year":"2023","journal-title":"Cell Genom."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"nwae188","DOI":"10.1093\/nsr\/nwae188","article-title":"A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice","volume":"11","author":"Li","year":"2024","journal-title":"Natl. Sci. Rev."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Bariah, I., Gribun, L., and Kashkush, K. (2022). Transposable elements are associated with genome-specific gene expression in bread wheat. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.1072232"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1016\/j.ajhg.2020.01.007","article-title":"Recurrent De Novo NAHR Reciprocal Duplications in the ATAD3 Gene Cluster Cause a Neurogenetic Trait with Perturbed Cholesterol and Mitochondrial Metabolism","volume":"106","author":"Gunning","year":"2020","journal-title":"Am. J. Hum. Genet."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/s13039-022-00600-6","article-title":"Mechanisms of structural chromosomal rearrangement formation","volume":"15","author":"Burssed","year":"2022","journal-title":"Mol. Cytogenet."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"e2322834121","DOI":"10.1073\/pnas.2322834121","article-title":"Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints","volume":"121","author":"Zhou","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1101\/gr.145631.112","article-title":"Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations","volume":"23","author":"Robberecht","year":"2013","journal-title":"Genome Res."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1111\/cge.14592","article-title":"Prenatal diagnosis of a 15q24.1 microdeletion in a fetus with cerebral and urogenital abnormalities","volume":"106","author":"Previdi","year":"2024","journal-title":"Clin. Genet."},{"key":"ref_82","first-page":"1","article-title":"The genomic basis of disease, mechanisms and assays for genomic disorders","volume":"1","author":"Stankiewicz","year":"2006","journal-title":"Genome Dyn."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"9703","DOI":"10.1093\/nar\/gkad650","article-title":"Recombinase-independent chromosomal rearrangements between dispersed inverted repeats in Saccharomyces cerevisiae meiosis","volume":"51","author":"Allison","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1111\/nph.70438","article-title":"Experimental insights into genome reconstruction driven by horizontal transfer of supernumerary chromosomes in Magnaporthe oryzae","volume":"248","author":"Fang","year":"2025","journal-title":"New Phytol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"5618","DOI":"10.1038\/s41467-026-71696-2","article-title":"Horizontal gene transfer and diploidy illuminate evolution and stress adaptation in oleaginous Scenedesmaceae (Chlorophyta)","volume":"17","author":"Li","year":"2026","journal-title":"Nat. Commun."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"e72653","DOI":"10.1002\/ece3.72653","article-title":"Reassessing Interkingdom Horizontal Gene Transfer Suggests Limited Influence on Plant Genomes","volume":"15","year":"2025","journal-title":"Ecol. Evol."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1089\/cmb.2007.A010","article-title":"Confounding factors in HGT detection: Statistical error, coalescent effects, and multiple solutions","volume":"14","author":"Than","year":"2007","journal-title":"J. Comput. Biol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"108197","DOI":"10.1016\/j.ympev.2024.108197","article-title":"Reticulate evolution: Detection and utility in the phylogenomics era","volume":"201","author":"Bjornson","year":"2024","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"jkae104","DOI":"10.1093\/g3journal\/jkae104","article-title":"Crossroads of assembling a moss genome: Navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana","volume":"14","author":"Vuruputoor","year":"2024","journal-title":"G3 (Bethesda)"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1038\/s41576-023-00688-5","article-title":"Horizontal gene transfer in eukaryotes: Aligning theory with data","volume":"25","author":"Keeling","year":"2024","journal-title":"Nat. Rev. Genet."},{"key":"ref_91","doi-asserted-by":"crossref","unstructured":"Aubin, E., El Baidouri, M., and Panaud, O. (2021). Horizontal Gene Transfers in Plants. Life, 11.","DOI":"10.3390\/life11080857"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"5377","DOI":"10.1038\/s41467-024-49679-y","article-title":"Impact of whole-genome duplications on structural variant evolution in Cochlearia","volume":"15","author":"Moore","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Ben\u00edtez-Ben\u00edtez, C., Mohan, A.V., S\u00e1nchez-Villegas, R., G\u00f3mez-Ramos, I., Vald\u00e9s-Florido, A., Lucek, K., Slov\u00e1k, M., Kol\u00e1\u0159, F., Leitch, I.J., and Luce\u00f1o, M. (2025). Bridging micro and macroevolution: Insights from chromosomal dynamics in plants. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1606450"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1007\/s11032-023-01396-y","article-title":"Polyploidy and diploidization in soybean","volume":"43","author":"Yuan","year":"2023","journal-title":"Mol. Breed."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"e2424854122","DOI":"10.1073\/pnas.2424854122","article-title":"Diploidization in a wild rice allopolyploid is both episodic and gradual","volume":"122","author":"Wang","year":"2025","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.pbi.2020.03.004","article-title":"One subgenome to rule them all: Underlying mechanisms of subgenome dominance","volume":"54","author":"Alger","year":"2020","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"1377","DOI":"10.1111\/nph.19656","article-title":"Convergent and\/or parallel evolution of RNA-binding proteins in angiosperms after polyploidization","volume":"242","author":"Guo","year":"2024","journal-title":"New Phytol."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"iyad114","DOI":"10.1093\/genetics\/iyad114","article-title":"Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus","volume":"225","author":"Bird","year":"2023","journal-title":"Genetics"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1016\/j.tig.2024.03.008","article-title":"Allopolyploid subgenome identification and implications for evolutionary analysis","volume":"40","author":"Session","year":"2024","journal-title":"Trends Genet."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1016\/j.tplants.2023.11.009","article-title":"Evolutionary insights into the organization of chromatin structure and landscape of transcriptional regulation in plants","volume":"29","author":"Long","year":"2024","journal-title":"Trends Plant Sci."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1146\/annurev-arplant-070122-030236","article-title":"cis-Regulatory Elements in Plant Development, Adaptation, and Evolution","volume":"74","author":"Marand","year":"2023","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_102","doi-asserted-by":"crossref","unstructured":"Horz, J.M., Wolff, K., Friedhoff, R., and Pucker, B. (2026). Genome sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation. BMC Genom., 27.","DOI":"10.1186\/s12864-026-12889-3"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1038\/s41586-024-08187-1","article-title":"Structural variation in the pangenome of wild and domesticated barley","volume":"636","author":"Jayakodi","year":"2024","journal-title":"Nature"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1186\/s13059-026-04028-8","article-title":"Comparative centromere genomics reveals evolutionary divergence in Solanaceae genomes","volume":"27","author":"Wan","year":"2026","journal-title":"Genome Biol."},{"key":"ref_105","doi-asserted-by":"crossref","unstructured":"Sapkota, M., Pereira, L., Wang, Y., Zhang, L., Topcu, Y., Tieman, D., and van der Knaap, E. (2023). Structural variation underlies functional diversity at methyl salicylate loci in tomato. PLoS Genet., 19.","DOI":"10.1371\/journal.pgen.1010751"},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1007\/s00122-023-04301-5","article-title":"Structural variation of GL1 gene determines the trichome formation in Brassica juncea","volume":"136","author":"Meng","year":"2023","journal-title":"Theor. Appl. Genet."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"1468","DOI":"10.1111\/pbi.14280","article-title":"Allelic variation of BBX24 is a dominant determinant controlling red coloration and dwarfism in pear","volume":"22","author":"Yang","year":"2024","journal-title":"Plant Biotechnol. J."},{"key":"ref_108","first-page":"giad064","article-title":"Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids","volume":"12","author":"Duong","year":"2023","journal-title":"GigaScience"},{"key":"ref_109","doi-asserted-by":"crossref","unstructured":"Zheng, X., Zhong, L., Pang, H., Wen, S., Li, F., Lou, D., Ge, J., Fan, W., Wang, T., and Han, Z. (2023). Lost genome segments associate with trait diversity during rice domestication. BMC Biol., 21.","DOI":"10.1186\/s12915-023-01512-6"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"2100","DOI":"10.1111\/pbi.14116","article-title":"Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs)","volume":"21","author":"Amas","year":"2023","journal-title":"Plant Biotechnol. J."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.jare.2023.03.006","article-title":"Gossypium purpurascens genome provides insight into the origin and domestication of upland cotton","volume":"56","author":"Cheng","year":"2024","journal-title":"J. Adv. Res."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1016\/j.tig.2026.01.002","article-title":"Sunflower genetics and genomics: From fundamental evolutionary insights to crop improvement","volume":"42","author":"Blackman","year":"2026","journal-title":"Trends Genet."},{"key":"ref_113","doi-asserted-by":"crossref","unstructured":"Long, X., Li, L., Fang, R., Zhang, J., Zhou, P., An, Z., Tang, W., Yao, J., and Wei, X. (2026). Pan-genome analysis of wax apple (Syzygium samarangense) and its association with fruit size and cold tolerance. Front. Plant Sci., 17.","DOI":"10.3389\/fpls.2026.1703197"},{"key":"ref_114","doi-asserted-by":"crossref","unstructured":"Zhong, H., Song, X., Chen, Q., Wang, L., Guo, J., Wang, B., Xie, Z., Niu, T., Shi, J., and Tang, M. (2026). Pan-genome landscape of the JAZ family in pepper (Capsicum annuum L.): Core-variable architecture and hormone crosstalk in leaves. Front. Plant Sci., 17.","DOI":"10.3389\/fpls.2026.1798486"},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"101231","DOI":"10.1016\/j.xplc.2024.101231","article-title":"Solanaceae pan-genomes reveal extensive fractionation and functional innovation of duplicated genes","volume":"6","author":"Zhang","year":"2025","journal-title":"Plant Commun."},{"key":"ref_116","doi-asserted-by":"crossref","unstructured":"Li, X., Dai, X., He, H., Chen, W., Qian, Q., Shang, L., Guo, L., and He, W. (2025). Uncovering the breeding contribution of transposable elements from landraces to improved varieties through pan-genome-wide analysis in rice. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1573546"},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s43897-022-00029-w","article-title":"Genomic structural variation in tomato and its role in plant immunity","volume":"2","author":"Jobson","year":"2022","journal-title":"Mol. Hortic."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"5487","DOI":"10.1038\/s41467-023-41251-4","article-title":"Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation","volume":"14","author":"Liu","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"101226","DOI":"10.1016\/j.xplc.2024.101226","article-title":"A comprehensive map of DNA-segment copy number variation in 491 genomes of common wheat uncovers genes associated with multiple agronomic traits","volume":"6","author":"Ma","year":"2025","journal-title":"Plant Commun."},{"key":"ref_120","doi-asserted-by":"crossref","unstructured":"Voelker, W.G., Krishnan, K., Chougule, K., Alexander, L.C., Lu, Z., Olson, A., Ware, D., Songsomboon, K., Ponce, C., and Brenton, Z.W. (2022). Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.1040909"},{"key":"ref_121","doi-asserted-by":"crossref","unstructured":"Tu, M., Zeng, J., Zhang, J., Fan, G., and Song, G. (2022). Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.1038109"},{"key":"ref_122","doi-asserted-by":"crossref","unstructured":"Wu, Y., Shi, H., Yu, H., Ma, Y., Hu, H., Han, Z., Zhang, Y., Zhen, Z., Yi, L., and Hou, J. (2022). Combined GWAS and Transcriptome Analyses Provide New Insights Into the Response Mechanisms of Sunflower Against Drought Stress. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.847435"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"e13899","DOI":"10.1111\/1755-0998.13899","article-title":"Leveraging whole-genome sequencing to estimate telomere length in plants","volume":"24","author":"Holliday","year":"2024","journal-title":"Mol. Ecol. Resour."},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/j.tplants.2018.11.008","article-title":"Next-Generation Sequencing Accelerates Crop Gene Discovery","volume":"24","author":"Nguyen","year":"2019","journal-title":"Trends Plant Sci."},{"key":"ref_125","doi-asserted-by":"crossref","unstructured":"Hong, K., Radian, Y., Manda, T., Xu, H., and Luo, Y. (2023). The Development of Plant Genome Sequencing Technology and Its Conservation and Application in Endangered Gymnosperms. Plants, 12.","DOI":"10.3390\/plants12234006"},{"key":"ref_126","doi-asserted-by":"crossref","unstructured":"Yanfang, Y., Wei, Z., Zijie, C., Yu, D., Shu, L., and Kai, Z. (2026). Genetic diversity and population differentiation of Parrotia subaequalis revealed by RAD-seq. Front. Plant Sci., 17.","DOI":"10.3389\/fpls.2026.1724975"},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-0716-3024-2_1","article-title":"Genotyping by Sequencing (GBS) for Genome-Wide SNP Identification in Plants","volume":"Volume 2638","author":"Pootakham","year":"2023","journal-title":"Plant Genotyping"},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"e17662","DOI":"10.1111\/mec.17662","article-title":"Structural Variants Contribute to Phenotypic Variation in Maize","volume":"34","author":"Catlin","year":"2025","journal-title":"Mol. Ecol."},{"key":"ref_129","doi-asserted-by":"crossref","unstructured":"Hotaling, S., Wilcox, E.R., Heckenhauer, J., Stewart, R.J., and Frandsen, P.B. (2023). Highly accurate long reads are crucial for realizing the potential of biodiversity genomics. BMC Genom., 24.","DOI":"10.1186\/s12864-023-09193-9"},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"5313","DOI":"10.1093\/jxb\/eraa263","article-title":"Oxford Nanopore sequencing: New opportunities for plant genomics?","volume":"71","author":"Dumschott","year":"2020","journal-title":"J. Exp. Bot."},{"key":"ref_131","doi-asserted-by":"crossref","unstructured":"Kyriakidou, M., Tai, H.H., Anglin, N.L., Ellis, D., and Str\u00f6mvik, M.V. (2018). Current Strategies of Polyploid Plant Genome Sequence Assembly. Front. Plant Sci., 9.","DOI":"10.3389\/fpls.2018.01660"},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"giaa146","DOI":"10.1093\/gigascience\/giaa146","article-title":"Comparison of long-read methods for sequencing and assembly of a plant genome","volume":"9","author":"Murigneux","year":"2020","journal-title":"GigaScience"},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1038\/s41587-019-0217-9","article-title":"Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome","volume":"37","author":"Wenger","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1111\/tpj.17011","article-title":"Structural variation discovery in wheat using PacBio high-fidelity sequencing","volume":"120","author":"Zhang","year":"2024","journal-title":"Plant J."},{"key":"ref_135","doi-asserted-by":"crossref","unstructured":"Tang, C., Yang, J., Yuan, S., and Li, Y. (2026). Chromosome-level genome assembly of Manglietia pachyphylla. Sci. Data.","DOI":"10.1038\/s41597-026-07475-x"},{"key":"ref_136","doi-asserted-by":"crossref","unstructured":"Chang, J.J.M., Ip, Y.C.A., Bauman, A.G., and Huang, D. (2020). MinION-in-ARMS: Nanopore Sequencing to Expedite Barcoding of Specimen-Rich Macrofaunal Samples From Autonomous Reef Monitoring Structures. Front. Mar. Sci., 7.","DOI":"10.3389\/fmars.2020.00448"},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"tpad158","DOI":"10.1093\/treephys\/tpad158","article-title":"Efficient selection of a biallelic and nonchimeric gene-edited tree using Oxford Nanopore Technologies sequencing","volume":"44","author":"Sato","year":"2024","journal-title":"Tree Physiol."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"100113","DOI":"10.1016\/j.xplc.2020.100113","article-title":"The chromosome-level reference genome assembly for Panax notoginseng and insights into ginsenoside biosynthesis","volume":"2","author":"Jiang","year":"2021","journal-title":"Plant Commun."},{"key":"ref_139","doi-asserted-by":"crossref","unstructured":"Lee, H., Chawla, H.S., Obermeier, C., Dreyer, F., Abbadi, A., and Snowdon, R. (2020). Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus. Front. Plant Sci., 11.","DOI":"10.3389\/fpls.2020.00496"},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/s13059-023-03160-z","article-title":"Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data","volume":"25","author":"Schrinner","year":"2024","journal-title":"Genome Biol."},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"102894","DOI":"10.1016\/j.pbi.2026.102894","article-title":"Revisiting tandem duplication in plant genomes: Technical challenges and pangenome solutions","volume":"91","author":"Lim","year":"2026","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_142","doi-asserted-by":"crossref","unstructured":"Yin, H., Yang, X., Zhan, D., Chen, Y., Pang, Z., and Wei, S. (2026). Haplotype-resolved telomere-to-telomere genome assembly of the hybrid Eucalyptus urophylla \u00d7 E. grandis. Sci. Data.","DOI":"10.1038\/s41597-026-07631-3"},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1038\/s41597-026-07044-2","article-title":"A near telomere-to-telomere chromosome-level genome assembly of Rhodiola yunnanensis (Crassulaceae)","volume":"13","author":"Wang","year":"2026","journal-title":"Sci. Data"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"e70223","DOI":"10.1111\/mpp.70223","article-title":"The Genome of the Rice Variety Mowanggu Provides Insight into Resistance to Magnaporthe oryzae","volume":"27","author":"Peng","year":"2026","journal-title":"Mol. Plant Pathol."},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"1689","DOI":"10.1038\/s41588-024-01826-3","article-title":"Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer","volume":"56","author":"Zhao","year":"2024","journal-title":"Nat. Genet."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"1648","DOI":"10.1093\/pcp\/pcab134","article-title":"Plant 3D Chromatin Organization: Important Insights from Chromosome Conformation Capture Analyses of the Last 10 Years","volume":"62","author":"Zhang","year":"2021","journal-title":"Plant Cell Physiol."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1038\/s41597-025-05322-z","article-title":"Haplotype-resolved chromosome-level genome assembly of Fragaria \u00d7 ananassa Duch. cv. \u2018Yuexin\u2019","volume":"12","author":"Lu","year":"2025","journal-title":"Sci. Data"},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"10105","DOI":"10.1038\/s41467-025-65065-8","article-title":"Conservation and variability of long-range interactions in structurally diverse maize genomes","volume":"16","author":"Liu","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_149","doi-asserted-by":"crossref","unstructured":"Diaz, I.A., Ostovar, T., Chen, J., de Dios, E.A., Piscatella, R., Perez-Alfaro, R.S., Zayed, O., Saddoris, S., Schmitz, R.J., and Wessler, S.R. (2025). A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus. BMC Genom., 26.","DOI":"10.1186\/s12864-025-12137-0"},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"1772","DOI":"10.1111\/nph.17262","article-title":"Plant 3D genomics: The exploration and application of chromatin organization","volume":"230","author":"Pei","year":"2021","journal-title":"New Phytol."},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"102599","DOI":"10.1016\/j.pbi.2024.102599","article-title":"The MVPs (masterful versatile players): Chromatin factors as pivotal mediators between 3D genome organization and the response to environment","volume":"81","author":"He","year":"2024","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1038\/s41588-024-01655-4","article-title":"Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea","volume":"56","author":"Li","year":"2024","journal-title":"Nat. Genet."},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"3405","DOI":"10.1016\/j.ygeno.2021.07.023","article-title":"Disruption of topologically associating domains by structural variations in tetraploid cottons","volume":"113","author":"Long","year":"2021","journal-title":"Genomics"},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"e14381","DOI":"10.1002\/advs.202514381","article-title":"Structural Variation and 3D Genome-Driven DNA\/RNA Methylation Divergence Contributing to Cotton Fiber Domestication","volume":"13","author":"Shao","year":"2026","journal-title":"Adv. Sci."},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"1430","DOI":"10.1093\/plcell\/koab081","article-title":"Altered chromatin architecture and gene expression during polyploidization and domestication of soybean","volume":"33","author":"Wang","year":"2021","journal-title":"Plant Cell"},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"2040","DOI":"10.1038\/s41588-026-02682-z","article-title":"Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber","volume":"58","author":"Guan","year":"2026","journal-title":"Nat. Genet."},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1038\/s41588-025-02462-1","article-title":"Graph pan-genome illuminates evolutionary trajectories and agronomic trait architecture in allotetraploid cotton","volume":"58","author":"Yang","year":"2026","journal-title":"Nat. Genet."},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"101835","DOI":"10.1016\/j.xplc.2026.101835","article-title":"NodeGWAS: Leveraging graph pangenomes for sensitive and accurate association analyses across diverse diploid and polyploid species","volume":"7","author":"Zhang","year":"2026","journal-title":"Plant Commun."},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1016\/j.molp.2025.08.001","article-title":"Varigraph: An accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes","volume":"18","author":"Du","year":"2025","journal-title":"Mol. Plant"},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"e20535","DOI":"10.1002\/tpg2.20535","article-title":"Brassica Panache: A multi-species graph pangenome representing presence absence variation across forty-one Brassica genomes","volume":"18","author":"MacNish","year":"2025","journal-title":"Plant Genome"},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"evae081","DOI":"10.1093\/gbe\/evae081","article-title":"Technological Development and Advances for Constructing and Analyzing Plant Pangenomes","volume":"16","author":"Hu","year":"2024","journal-title":"Genome Biol. Evol."},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1186\/s13059-025-03606-6","article-title":"A survey of sequence-to-graph mapping algorithms in the pangenome era","volume":"26","author":"Cui","year":"2025","journal-title":"Genome Biol."},{"key":"ref_163","doi-asserted-by":"crossref","unstructured":"Rice, E.S., Alberdi, A., Alfieri, J., Athrey, G., Balacco, J.R., Bardou, P., Blackmon, H., Charles, M., Cheng, H.H., and Fedrigo, O. (2023). A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. BMC Biol., 21.","DOI":"10.1186\/s12915-023-01758-0"},{"key":"ref_164","doi-asserted-by":"crossref","unstructured":"Wang, L., Kan, J., Zhong, W., Zhang, S., Zhao, Y., Hou, Y., Tembrock, L.R., Gu, X., and Cheng, Y. (2026). From High-Density Genomic Mapping to Precision Molecular Breeding: A Comprehensive Review of Capsicum Genomic Resources. Genes, 17.","DOI":"10.3390\/genes17030298"},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"uhac210","DOI":"10.1093\/hr\/uhac210","article-title":"High-quality chromosome-scale genomes facilitate effective identification of large structural variations in hot and sweet peppers","volume":"9","author":"Lee","year":"2022","journal-title":"Hortic. Res."},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1094\/MPMI-10-25-0150-FI","article-title":"Modern Genomics Reshapes Soybean Cyst Nematode Research: Integrating Host Resistance, Nematode Virulence, and Functional Discovery","volume":"39","author":"Miraeiz","year":"2026","journal-title":"Mol. Plant Microbe Interact."},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1007\/s00122-025-05020-9","article-title":"Identification of new genomic loci for seed protein and oil content in the soybean pangenome using genome-wide association and haplotype analyses","volume":"138","author":"Vuong","year":"2025","journal-title":"Theor. Appl. Genet."},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"103418","DOI":"10.1016\/j.copbio.2025.103418","article-title":"Functional cereal pan-genomics: Harnessing structural and regulatory variation for precision crop design","volume":"97","author":"Zhu","year":"2026","journal-title":"Curr. Opin. Biotechnol."},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1186\/s13059-026-04058-2","article-title":"The pan-genome provides insights into evolutionary dynamics and fatty acid metabolism in Aceraceae family","volume":"27","author":"Ma","year":"2026","journal-title":"Genome Biol."},{"key":"ref_170","doi-asserted-by":"crossref","unstructured":"Alc\u00e1ntar-Aguirre, F.C., Zamora-Macorra, E.J., Guti\u00e9rrez, U.V., Carrillo-Tripp, J., Diaz-Lara, A., and Avi\u00f1a-Padilla, K. (2026). Mexico as a hotspot for plant virus evolution: Eco-evolutionary regimes shaping viral emergence. Front. Plant Sci., 17.","DOI":"10.3389\/fpls.2026.1800439"},{"key":"ref_171","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1186\/s13059-024-03239-1","article-title":"A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline","volume":"25","author":"Du","year":"2024","journal-title":"Genome Biol."},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"1720","DOI":"10.1101\/gr.236273.118","article-title":"Chromosome assembly of large and complex genomes using multiple references","volume":"28","author":"Kolmogorov","year":"2018","journal-title":"Genome Res."},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_174","doi-asserted-by":"crossref","first-page":"110568","DOI":"10.1016\/j.ygeno.2023.110568","article-title":"Benchmarking of structural variant detection in the tetraploid potato genome using linked-read sequencing","volume":"115","author":"Weisweiler","year":"2023","journal-title":"Genomics"},{"key":"ref_175","doi-asserted-by":"crossref","first-page":"bbae441","DOI":"10.1093\/bib\/bbae441","article-title":"Comprehensive assessment of long-read sequencing platforms and calling algorithms for detection of copy number variation","volume":"25","author":"Yuan","year":"2024","journal-title":"Brief. Bioinform."},{"key":"ref_176","doi-asserted-by":"crossref","unstructured":"Pei, Y., Tanguy, M., Giess, A., Dixit, A., Wilson, L.C., Gibbons, R.J., Twigg, S.R.F., Elgar, G., and Wilkie, A.O.M. (2024). A Comparison of Structural Variant Calling from Short-Read and Nanopore-Based Whole-Genome Sequencing Using Optical Genome Mapping as a Benchmark. Genes, 15.","DOI":"10.3390\/genes15070925"},{"key":"ref_177","doi-asserted-by":"crossref","unstructured":"Nkouamedjo Fankep, R.C., S\u00f6ylev, A., Kobiela, A.-L., Blom, J., Ernst, C., and Motameny, S. (2025). SV-MeCa: An XGBoost-based meta-caller approach for structural variant calling from short-read data. BMC Bioinform., 26.","DOI":"10.1186\/s12859-025-06246-6"},{"key":"ref_178","doi-asserted-by":"crossref","first-page":"bbae462","DOI":"10.1093\/bib\/bbae462","article-title":"VISTA: An integrated framework for structural variant discovery","volume":"25","author":"Sarwal","year":"2024","journal-title":"Brief. Bioinform."},{"key":"ref_179","doi-asserted-by":"crossref","unstructured":"Liu, C., Xu, H., Li, Z., Wang, Y., Zhang, J., Qiao, S., and Zhang, H. (2025). From map to blueprint: The plant pan-genome unraveling genetic mysteries and powering precision breeding. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1673637"},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"giaf121","DOI":"10.1093\/gigascience\/giaf121","article-title":"Toward a standardized framework for pangenome graph evaluation: Assessing crop plant pangenome variation graph construction from multiple assemblies","volume":"14","author":"Kopalli","year":"2025","journal-title":"Gigascience"},{"key":"ref_181","doi-asserted-by":"crossref","first-page":"20210032","DOI":"10.1515\/jib-2021-0032","article-title":"Fast alignment of reads to a variation graph with application to SNP detection","volume":"18","author":"Monsu","year":"2021","journal-title":"J. Integr. Bioinform."},{"key":"ref_182","doi-asserted-by":"crossref","unstructured":"Zhang, K.L., Leng, Y.N., Hao, R.R., Zhang, W.Y., Li, H.F., Chen, M.X., and Zhu, F.Y. (2024). Adaptation of High-Altitude Plants to Harsh Environments: Application of Phenotypic-Variation-Related Methods and Multi-Omics Techniques. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms252312666"},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1016\/j.jgg.2022.06.004","article-title":"Plant pan-genomics: Recent advances, new challenges, and roads ahead","volume":"49","author":"Li","year":"2022","journal-title":"J. Genet. Genom."},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"101032","DOI":"10.1016\/j.xgen.2025.101032","article-title":"Multi-omic underpinnings of heterogeneous aging across multiple organ systems","volume":"5","author":"Xiong","year":"2025","journal-title":"Cell Genom."},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"8652","DOI":"10.1038\/s41467-024-53044-4","article-title":"Integrative multi-omics analysis reveals genetic and heterotic contributions to male fertility and yield in potato","volume":"15","author":"Li","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_186","doi-asserted-by":"crossref","first-page":"2538","DOI":"10.1038\/s41588-024-01957-7","article-title":"Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions","volume":"56","author":"Zhang","year":"2024","journal-title":"Nat. Genet."},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1007\/s00122-025-04867-2","article-title":"Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus","volume":"138","author":"Yildiz","year":"2025","journal-title":"Theor. Appl. Genet."},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"3023","DOI":"10.1534\/g3.119.400549","article-title":"Transcriptome-Wide Association Supplements Genome-Wide Association in Zea mays","volume":"9","author":"Kremling","year":"2019","journal-title":"G3 (Bethesda)"},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"1205","DOI":"10.1038\/s41477-025-02007-8","article-title":"Transcription factor binding divergence drives transcriptional and phenotypic variation in maize","volume":"11","author":"Galli","year":"2025","journal-title":"Nat. Plants"},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"kiaf468","DOI":"10.1093\/plphys\/kiaf468","article-title":"Vegetative to generative1 (Vgt1) is an enhancer affecting flowering time and jasmonate signaling in maize by promoting the expression of Zea mays Related to APETALA 2.7","volume":"199","author":"Zicola","year":"2025","journal-title":"Plant Physiol."},{"key":"ref_191","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1016\/j.cell.2022.04.003","article-title":"Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays","volume":"185","author":"Chen","year":"2022","journal-title":"Cell"},{"key":"ref_192","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1016\/j.molp.2025.02.003","article-title":"A large-scale integrated transcriptomic atlas for soybean organ development","volume":"18","author":"Fan","year":"2025","journal-title":"Mol. Plant"},{"key":"ref_193","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.tplants.2023.10.002","article-title":"Introducing single cell stereo-sequencing technology to transform the plant transcriptome landscape","volume":"29","author":"Bawa","year":"2024","journal-title":"Trends Plant Sci."},{"key":"ref_194","doi-asserted-by":"crossref","unstructured":"Li, Y., Kong, L., Guo, X., Chen, Y., Shao, W., Liu, M., Luo, C., Liang, S., Feng, A., and Xu, L. (J. Genet. Genom., 2026). A single-nucleus and spatial transcriptomic atlas of poplar leaves reveals the regulation of leaf polarity and cuticle deposition, J. Genet. Genom., in press.","DOI":"10.1016\/j.jgg.2026.03.015"},{"key":"ref_195","doi-asserted-by":"crossref","unstructured":"Li, Y., Vigil, J., Pradhan, R., Zhu, J., and Libault, M. (2026). Integrating Single-Cell and Spatial Multi-Omics to Decode Plant-Microbe Interactions at Cellular Resolution. Microorganisms, 14.","DOI":"10.3390\/microorganisms14020380"},{"key":"ref_196","doi-asserted-by":"crossref","first-page":"1362","DOI":"10.1016\/j.molp.2021.05.028","article-title":"Reconstruction of lateral root formation through single-cell RNA sequencing reveals order of tissue initiation","volume":"14","author":"Gude","year":"2021","journal-title":"Mol. Plant"},{"key":"ref_197","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1105\/tpc.18.00785","article-title":"Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana","volume":"31","author":"Alexandre","year":"2019","journal-title":"Plant Cell"},{"key":"ref_198","doi-asserted-by":"crossref","unstructured":"Zhao, N., Ding, X., Tian, C., Wang, S., Xie, S., Zou, H., Liu, H., Chen, J., Lian Liang, X., and Huang, L. (2024). Transcriptional landscape of sweetpotato root tip development at the single-cell level. BMC Plant Biol., 24.","DOI":"10.1186\/s12870-024-05574-8"},{"key":"ref_199","doi-asserted-by":"crossref","first-page":"2838","DOI":"10.1038\/s41467-022-30177-y","article-title":"A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data","volume":"13","author":"Neumann","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_200","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1111\/tpj.15458","article-title":"Single-nucleus RNA sequencing of plant tissues using a nanowell-based system","volume":"108","author":"Muino","year":"2021","journal-title":"Plant J."},{"key":"ref_201","doi-asserted-by":"crossref","first-page":"1839","DOI":"10.1111\/pbi.14097","article-title":"Single-cell RNA sequencing profiles reveal cell type-specific transcriptional regulation networks conditioning fungal invasion in maize roots","volume":"21","author":"Cao","year":"2023","journal-title":"Plant Biotechnol. J."},{"key":"ref_202","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1111\/tpj.16487","article-title":"Single-cell transcriptomic analysis of pea shoot development and cell-type-specific responses to boron deficiency","volume":"117","author":"Chen","year":"2024","journal-title":"Plant J."},{"key":"ref_203","first-page":"581774","article-title":"Plant-Derived Exosome-Like Nanoparticles: Mechanisms of Cross-Kingdom Regulation and Perspectives as Natural Drug Carriers for Disease Treatment","volume":"21","author":"Liu","year":"2026","journal-title":"Int. J. Nanomed."},{"key":"ref_204","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1038\/s41592-021-01282-5","article-title":"Single-cell chromatin state analysis with Signac","volume":"18","author":"Stuart","year":"2021","journal-title":"Nat. Methods"},{"key":"ref_205","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"ref_206","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/s41592-021-01358-2","article-title":"Squidpy: A scalable framework for spatial omics analysis","volume":"19","author":"Palla","year":"2022","journal-title":"Nat. Methods"},{"key":"ref_207","doi-asserted-by":"crossref","first-page":"bbaf723","DOI":"10.1093\/bib\/bbaf723","article-title":"Advances and challenges in single-cell RNA sequencing data analysis: A comprehensive review","volume":"27","author":"Nesari","year":"2026","journal-title":"Brief. Bioinform."},{"key":"ref_208","doi-asserted-by":"crossref","first-page":"2461","DOI":"10.1038\/s41477-025-02160-0","article-title":"Advances and prospects of large DNA fragment editing in plants","volume":"11","author":"Zhao","year":"2025","journal-title":"Nat. Plants"},{"key":"ref_209","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1038\/s41586-022-04808-9","article-title":"Graph pangenome captures missing heritability and empowers tomato breeding","volume":"606","author":"Zhou","year":"2022","journal-title":"Nature"},{"key":"ref_210","doi-asserted-by":"crossref","unstructured":"Silaiyiman, S., Liu, J., Wu, J., Ouyang, L., Cao, Z., and Shen, C. (2025). A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes. Plants, 14.","DOI":"10.3390\/plants14091399"},{"key":"ref_211","doi-asserted-by":"crossref","unstructured":"Diakite, S., Norman, P.E., Kamara, L., Pehlivan, N., and Zargar, M. (2026). Genetic enhancement of root, tuber and cereal crops via pangenomics, multi-omics integration and AI-driven prediction. Front. Plant Sci., 17.","DOI":"10.3389\/fpls.2026.1793924"},{"key":"ref_212","doi-asserted-by":"crossref","unstructured":"Stephens, Z.D., Lee, S.Y., Faghri, F., Campbell, R.H., Zhai, C., Efron, M.J., Iyer, R., Schatz, M.C., Sinha, S., and Robinson, G.E. (2015). Big Data: Astronomical or Genomical?. PLoS Biol., 13.","DOI":"10.1371\/journal.pbio.1002195"},{"key":"ref_213","doi-asserted-by":"crossref","first-page":"20230012","DOI":"10.1515\/jib-2023-0012","article-title":"Integrating omics databases for enhanced crop breeding","volume":"20","author":"Chao","year":"2023","journal-title":"J. Integr. Bioinform."},{"key":"ref_214","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1007\/s00122-025-05080-x","article-title":"Low-call-rate SNPs and presence-absence variation identified in the rice pan-genome can improve genomic prediction of rice gene bank accessions","volume":"138","author":"Krusenbaum","year":"2025","journal-title":"Theor. Appl. Genet."},{"key":"ref_215","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1007\/s00122-025-05044-1","article-title":"RsRCO and RsLMI1 co-regulate the formation of lobed leaf in radish (Raphanus sativus L.)","volume":"138","author":"Yang","year":"2025","journal-title":"Theor. Appl. Genet."},{"key":"ref_216","doi-asserted-by":"crossref","first-page":"111778","DOI":"10.1016\/j.plantsci.2023.111778","article-title":"Genome-wide presence\/absence variation discovery and its application in Peach (Prunus persica)","volume":"335","author":"Bie","year":"2023","journal-title":"Plant Sci."},{"key":"ref_217","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1038\/s42003-026-09850-1","article-title":"Subspecies-specific haplotype signatures for customizing blanchability in groundnut (Arachis hypogaea L.) via haplotype-based breeding","volume":"9","author":"Shah","year":"2026","journal-title":"Commun. Biol."},{"key":"ref_218","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1007\/s00122-018-3215-2","article-title":"Modeling copy number variation in the genomic prediction of maize hybrids","volume":"132","author":"Lyra","year":"2019","journal-title":"Theor. Appl. Genet."},{"key":"ref_219","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1007\/s42994-025-00206-7","article-title":"Plant graph-based pangenomics: Techniques, applications, and challenges","volume":"6","author":"Du","year":"2025","journal-title":"aBIOTECH"},{"key":"ref_220","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1007\/s00122-026-05201-0","article-title":"Accessing crop genetic diversity via pangenomics","volume":"139","author":"MacNish","year":"2026","journal-title":"Theor. Appl. Genet."},{"key":"ref_221","doi-asserted-by":"crossref","unstructured":"Zhou, R., Jiang, F., Niu, L., Song, X., Yu, L., Yang, Y., and Wu, Z. (2022). Increase Crop Resilience to Heat Stress Using Omic Strategies. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.891861"},{"key":"ref_222","doi-asserted-by":"crossref","unstructured":"Zenda, T., Liu, S., Dong, A., Li, J., Wang, Y., Liu, X., Wang, N., and Duan, H. (2021). Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.774994"},{"key":"ref_223","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1080\/14789450.2018.1476143","article-title":"Integrative omics\u2014From data to biology","volume":"15","author":"Dihazi","year":"2018","journal-title":"Expert Rev. Proteom."},{"key":"ref_224","doi-asserted-by":"crossref","first-page":"3507","DOI":"10.1007\/s00253-022-11963-6","article-title":"Machine learning: Its challenges and opportunities in plant system biology","volume":"106","author":"Hesami","year":"2022","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_225","doi-asserted-by":"crossref","first-page":"3679","DOI":"10.1111\/pbi.70591","article-title":"Challenges in Bringing Pangenome Research Into Breeding: A Case Study in Rice","volume":"24","author":"Nie","year":"2026","journal-title":"Plant Biotechnol. J."},{"key":"ref_226","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1007\/s00122-025-04973-1","article-title":"In silico prediction of variant effects: Promises and limitations for precision plant breeding","volume":"138","author":"Sendrowski","year":"2025","journal-title":"Theor. Appl. Genet."},{"key":"ref_227","doi-asserted-by":"crossref","first-page":"101010","DOI":"10.1016\/j.xplc.2024.101010","article-title":"TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean","volume":"5","author":"Li","year":"2024","journal-title":"Plant Commun."},{"key":"ref_228","doi-asserted-by":"crossref","first-page":"uhae106","DOI":"10.1093\/hr\/uhae106","article-title":"A phased genome of the highly heterozygous \u2018Texas\u2019 almond uncovers patterns of allele-specific expression linked to heterozygous structural variants","volume":"11","author":"Castanera","year":"2024","journal-title":"Hortic. Res."},{"key":"ref_229","doi-asserted-by":"crossref","unstructured":"Yang, Y., Saand, M.A., Huang, L., Abdelaal, W.B., Zhang, J., Wu, Y., Li, J., Sirohi, M.H., and Wang, F. (2021). Applications of Multi-Omics Technologies for Crop Improvement. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.563953"},{"key":"ref_230","doi-asserted-by":"crossref","first-page":"102786","DOI":"10.1016\/j.pbi.2025.102786","article-title":"Fine-scale 3D chromatin architectures and their regulatory mechanisms in plants","volume":"88","author":"Xiao","year":"2025","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_231","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1016\/j.tplants.2024.03.007","article-title":"The era of panomics-driven gene discovery in plants","volume":"29","author":"Mishra","year":"2024","journal-title":"Trends Plant Sci."},{"key":"ref_232","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1111\/jipb.13841","article-title":"Navigating the landscape of plant proteomics","volume":"67","author":"Sang","year":"2025","journal-title":"J. Integr. Plant Biol."},{"key":"ref_233","doi-asserted-by":"crossref","unstructured":"Halder, T., Bhoite, R., Islam, S., Yan, G., Siddiqui, M.N., Kayess, M.O., and Siddique, K.H.M. (2025). Proteomics in Allopolyploid Crops: Stress Resilience, Challenges and Prospects. Proteomes, 13.","DOI":"10.20944\/preprints202510.1553.v1"},{"key":"ref_234","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1016\/j.molp.2025.01.017","article-title":"Graph-based pangenome provides insights into structural variations and genetic basis of metabolic traits in potato","volume":"18","author":"Zhu","year":"2025","journal-title":"Mol. Plant"},{"key":"ref_235","doi-asserted-by":"crossref","first-page":"4999","DOI":"10.1111\/mec.17088","article-title":"Evolutionary roles of polyploidization-derived structural variations in the phenotypic diversification of Panax species","volume":"32","author":"Zhang","year":"2023","journal-title":"Mol. Ecol."},{"key":"ref_236","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1016\/j.pld.2025.12.012","article-title":"Genomic insights into alpine plant adaptation","volume":"48","author":"Zhang","year":"2026","journal-title":"Plant Divers."},{"key":"ref_237","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1007\/s44154-025-00260-7","article-title":"Plant-pathogen interactions: Making the case for multi-omics analysis of complex pathosystems","volume":"5","author":"Balotf","year":"2025","journal-title":"Stress Biol."},{"key":"ref_238","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1042\/ETLS20200274","article-title":"Space: The final frontier\u2014Achieving single-cell, spatially resolved transcriptomics in plants","volume":"5","author":"Gurazada","year":"2021","journal-title":"Emerg. Top. Life Sci."},{"key":"ref_239","doi-asserted-by":"crossref","first-page":"100508","DOI":"10.1016\/j.xplc.2022.100508","article-title":"Single-cell and spatial multi-omics in the plant sciences: Technical advances, applications, and perspectives","volume":"4","author":"Yu","year":"2023","journal-title":"Plant Commun."},{"key":"ref_240","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1016\/j.molp.2026.03.016","article-title":"Single-cell and haplotype-resolved transcriptomics reveal molecular signatures of orchid floral structures","volume":"19","author":"Li","year":"2026","journal-title":"Mol. Plant"},{"key":"ref_241","doi-asserted-by":"crossref","first-page":"1714","DOI":"10.1038\/s41477-025-02088-5","article-title":"Genome analyses and breeding of polyploid crops","volume":"11","author":"Cheng","year":"2025","journal-title":"Nat. Plants"},{"key":"ref_242","doi-asserted-by":"crossref","first-page":"uhaf107","DOI":"10.1093\/hr\/uhaf107","article-title":"The nature of complex structural variations in tomatoes","volume":"12","author":"Cui","year":"2025","journal-title":"Hortic. Res."},{"key":"ref_243","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1007\/s00122-025-05010-x","article-title":"Climate change and plant genomic plasticity","volume":"138","author":"Pozzi","year":"2025","journal-title":"Theor. Appl. Genet."},{"key":"ref_244","doi-asserted-by":"crossref","unstructured":"Shi, J., Lu, Y., Sheng, Z., Liu, H., Li, K., Chong, Y., Gao, Z., Deng, W., and Wu, D. (2026). Pangenomics for Agricultural Breeding: Construction Strategies, Evidence Integration, and Translational Constraints. Biology, 15.","DOI":"10.3390\/biology15110832"},{"key":"ref_245","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/j.tplants.2022.08.018","article-title":"Machine learning bridges omics sciences and plant breeding","volume":"28","author":"Yan","year":"2023","journal-title":"Trends Plant Sci."},{"key":"ref_246","doi-asserted-by":"crossref","first-page":"102825","DOI":"10.1016\/j.pbi.2025.102825","article-title":"Pangenomics combined with artificial intelligence and precision breeding can accelerate crop improvement","volume":"88","author":"Li","year":"2025","journal-title":"Curr. Opin. 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