{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T09:22:17Z","timestamp":1788340937084,"version":"build-2803163510"},"reference-count":47,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T00:00:00Z","timestamp":1788307200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"Joint the Fund for Forestry and Grassland Science of the National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["U2571217"],"award-info":[{"award-number":["U2571217"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["U2571217"],"award-info":[{"award-number":["U2571217"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Henan Provincial Financial Science and Technology Forestry Promotion Project","award":["32030008"],"award-info":[{"award-number":["32030008"]}]},{"name":"Joint Fund of Henan Province Science and Technology Research and Development Plan (Applied Research and Development Category) Project","award":["242103810016"],"award-info":[{"award-number":["242103810016"]}]},{"name":"Henan Province Enterprise-University Cooperation Center of I. polycarpa Project","award":["30803680"],"award-info":[{"award-number":["30803680"]}]},{"name":"Henan Provincial Science and Technology Tackling Project","award":["252102110233"],"award-info":[{"award-number":["252102110233"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Idesia polycarpa is a woody oil tree threatened by stem canker caused by Botryosphaeria dothidea, yet the organization and infection-responsive behavior of its phenylalanine ammonia-lyase (PAL) gene family remain poorly understood. Here, we identified five IpPAL genes and characterized their phylogenetic relationships, conserved features, duplication patterns, promoter cis-elements, and infection-associated expression profiles. Segmental and tandem duplication contributed to IpPAL family evolution, and all duplicated pairs showed Ka\/Ks ratios below 1, consistent with purifying selection. RNA sequencing (RNA-seq) of contrasting Chengdu and Zhangjiajie provenances revealed distinct temporal responses. In Chengdu, IpPAL2\u2013IpPAL4 were significantly upregulated at 24 h after inoculation, whereas all five genes were upregulated at 96 h. In Zhangjiajie, all five IpPAL genes were significantly upregulated at 24 h, while IpPAL2\u2013IpPAL5 remained upregulated at 96 h. No IpPAL gene met the differential-expression criteria between provenances under mock conditions or at 24 h; at 96 h, IpPAL1 and IpPAL3 were lower and IpPAL5 was higher in Zhangjiajie than in Chengdu. Scanning electron microscopy (SEM) provided complementary qualitative evidence of provenance-associated tissue responses. These findings demonstrate time- and gene-specific IpPAL responses to B. dothidea and identify candidate genes for further functional analysis.<\/jats:p>","DOI":"10.3390\/ijms27177842","type":"journal-article","created":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T08:56:01Z","timestamp":1788339361000},"page":"7842","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome-Wide Identification of the PAL Gene Family in Idesia\u00a0polycarpa and Transcriptomic Responses to Botryosphaeria\u00a0dothidea Infection"],"prefix":"10.3390","volume":"27","author":[{"given":"Ming","family":"Liu","sequence":"first","affiliation":[{"name":"College of Forestry, Henan Agricultural University, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-2016-3126","authenticated-orcid":false,"given":"Qiuliang","family":"Chi","sequence":"additional","affiliation":[{"name":"College of Forestry, Henan Agricultural University, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Zhao","sequence":"additional","affiliation":[{"name":"Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisha","family":"Fang","sequence":"additional","affiliation":[{"name":"College of Forestry, Xinyang Agriculture and Forestry University, Xinyang 464000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Dai","sequence":"additional","affiliation":[{"name":"College of Forestry, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"National Forestry and Grassland Administration Key Laboratory for Central Plains Forest Resources Cultivation, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"Henan Province Engineering Technology Research Center for Idesia, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5612-9477","authenticated-orcid":false,"given":"Zhi","family":"Li","sequence":"additional","affiliation":[{"name":"College of Forestry, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"National Forestry and Grassland Administration Key Laboratory for Central Plains Forest Resources Cultivation, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"Henan Province Engineering Technology Research Center for Idesia, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaodong","family":"Geng","sequence":"additional","affiliation":[{"name":"College of Forestry, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"National Forestry and Grassland Administration Key Laboratory for Central Plains Forest Resources Cultivation, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"Henan Province Engineering Technology Research Center for Idesia, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Forestry, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"National Forestry and Grassland Administration Key Laboratory for Central Plains Forest Resources Cultivation, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"Henan Province Engineering Technology Research Center for Idesia, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongyu","family":"Ren","sequence":"additional","affiliation":[{"name":"College of Forestry, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"National Forestry and Grassland Administration Key Laboratory for Central Plains Forest Resources Cultivation, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"Henan Province Engineering Technology Research Center for Idesia, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanmei","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Forestry, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"National Forestry and Grassland Administration Key Laboratory for Central Plains Forest Resources Cultivation, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"Henan Province Engineering Technology Research Center for Idesia, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Forestry, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"National Forestry and Grassland Administration Key Laboratory for Central Plains Forest Resources Cultivation, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"Henan Province Engineering Technology Research Center for Idesia, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-4103-7553","authenticated-orcid":false,"given":"Fangming","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Forestry, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"National Forestry and Grassland Administration Key Laboratory for Central Plains Forest Resources Cultivation, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"Henan Province Engineering Technology Research Center for Idesia, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6766-7406","authenticated-orcid":false,"given":"Qifei","family":"Cai","sequence":"additional","affiliation":[{"name":"College of Forestry, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"National Forestry and Grassland Administration Key Laboratory for Central Plains Forest Resources Cultivation, Henan Agricultural University, Zhengzhou 450046, China"},{"name":"Henan Province Engineering Technology Research Center for Idesia, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Fu, X., Luo, J., Guo, Y., Feng, D., Deng, Y., Kuang, M., Zhou, H., Liu, X., and Sun, C. (2025). The Complete Chloroplast Genome of Idesia polycarpa and Comparative Analysis of Related Species. Genes, 16.","DOI":"10.3390\/genes16050611"},{"key":"ref_2","first-page":"44","article-title":"Research progress and industrial application prospects of Idesia polycarpa oil","volume":"34","author":"Liu","year":"2026","journal-title":"J. Grain Oil Food Sci. Technol."},{"key":"ref_3","first-page":"29","article-title":"Development and utilization of woody oil tree species Idesia polycarpa","volume":"46","author":"Wang","year":"2017","journal-title":"Hubei For. Sci. Technol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1372","DOI":"10.1111\/ppa.13895","article-title":"Botryosphaeria Dothidea Causes Stem Canker of Idesia Polycarpa in China","volume":"73","author":"Fang","year":"2024","journal-title":"Plant Pathol."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Yuan, Q., Zhu, Y., Yang, Y., Miao, C., Zhong, W., Hu, Z., Chen, C., Liu, Z., Wang, Y., and Geng, X. (2025). Physiological and Biochemical Responses of Idesia Polycarpa to Botryosphaeria Dothidea Infection at Different Stages of Stem Canker Disease. Forests, 16.","DOI":"10.3390\/f16091411"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Yadav, V., Wang, Z., Wei, C., Amo, A., Ahmed, B., Yang, X., and Zhang, X. (2020). Phenylpropanoid Pathway Engineering: An Emerging Approach towards Plant Defense. Pathogens, 9.","DOI":"10.3390\/pathogens9040312"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Xing, F., Zhang, L., Ge, W., Fan, H., Tian, C., and Meng, F. (2024). Comparative Transcriptome Analysis Reveals the Importance of Phenylpropanoid Biosynthesis for the Induced Resistance of 84K Poplar to Anthracnose. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10209-1"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Chen, X., Jiang, C., Long, M., Hu, X., Xu, S., Huo, H., Shi, R., Xu, Q., Xie, S., and Li, Z. (2025). Overexpression of the Glycyr-rhiza Uralensis Phenylalanine Ammonia-Lyase Gene GuPAL1 Promotes Flavonoid Accumulation in Arabidopsis Thaliana. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26094073"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Zhang, H., Zhang, X., Zhao, H., Hu, J., Wang, Z., Yang, G., Zhou, X., and Wan, H. (2023). Genome-Wide Identification and Ex-pression Analysis of Phenylalanine Ammonia-Lyase (PAL) Family in Rapeseed (Brassica napus L.). BMC Plant Biol., 23.","DOI":"10.1186\/s12870-023-04472-9"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1007\/s11816-025-01017-4","article-title":"Genome-Wide Identification of PAL Family Genes and Their Response to Cold Stress in Poncirus Trifoliata","volume":"19","author":"Hu","year":"2025","journal-title":"Plant Biotechnol. Rep."},{"key":"ref_11","first-page":"172","article-title":"Identification and expression pattern analysis of the PAL gene family in Arabidopsis thaliana","volume":"59","author":"Qin","year":"2022","journal-title":"J. Sichuan Univ. (Nat. Sci. Ed.)"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1071\/CP21558","article-title":"Molecular Characterisation of PAL Gene Family Reveals Their Role in Abiotic Stress Response in Lucerne (Medicago sativa)","volume":"73","author":"Feng","year":"2022","journal-title":"Crop Pasture Sci."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Song, S., Huang, S., Tian, C., Zhao, Y., Qin, Y., and Liao, H. (2022). Phenylalanine ammonia lyase GmPAL1.1 promotes seed vigor under high-temperature and -humidity stress and enhances seed germination under salt and drought stress in transgenic Arabidopsis. Plants, 11.","DOI":"10.3390\/plants11233239"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Shen, D., Diao, J., Lin, H., Zhou, W., Ma, W., Dong, A., and Ma, L. (2026). Enhanced resistance to Botryosphaeria dothidea through upregulation of the lignin biosynthesis regulator WRKY11 in poplar. Front. Plant Sci., 17.","DOI":"10.3389\/fpls.2026.1737207"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"14059","DOI":"10.1038\/s41598-018-32204-9","article-title":"Salicylic acid in Populus tomentosa is a remote signalling molecule induced by Botryosphaeria dothidea infection","volume":"8","author":"Li","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Li, C., Zhang, G., Cheng, G., and Wang, Q. (2025). Phenylalanine Ammonia-Lyase GhPAL9 Confers Resistance to Verticillium Wilt in Cotton. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26114983"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Liu, R., Lv, X., Wang, X.H., Yang, L., Cao, J., Dai, Y., Wu, W., and Wu, Y. (2023). Integrative analysis of the multi-omics reveals the stripe rust fungus resistance mechanism of the TaPAL in wheat. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1174450"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"e70582","DOI":"10.1111\/tpj.70582","article-title":"The TaNAC29L-B\u2013TaNAC1L-a Module Negatively Regulates Wheat Sharp Eyespot Resistance by Reducing Lignin Content Though the Phenylalanine Ammonia-Lyase Gene TaPAL4-B","volume":"124","author":"Gao","year":"2025","journal-title":"Plant J."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"uhad213","DOI":"10.1093\/hr\/uhad213","article-title":"Red light induces salicylic acid accumulation by activating CaHY5 to enhance pepper resistance against Phytophthora capsici","volume":"10","author":"Yang","year":"2023","journal-title":"Hortic. Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1038\/s41586-025-09175-9","article-title":"Complete Biosynthesis of Salicylic Acid from Phenylalanine in Plants","volume":"645","author":"Zhu","year":"2025","journal-title":"Nature"},{"key":"ref_21","first-page":"2265","article-title":"Gene family analysis of phenylalanine ammonia-lyase (PAL) and functional study of ZmPAL5 in maize","volume":"57","author":"Cao","year":"2024","journal-title":"Sci. Agric. Sin."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1526","DOI":"10.1104\/pp.110.157370","article-title":"Functional Analysis of the Arabidopsis PAL Gene Family in Plant Growth, Development, and Response to Environmental Stress","volume":"153","author":"Huang","year":"2010","journal-title":"Plant Physiol."},{"key":"ref_23","unstructured":"Hou, P., Liang, D., Zhang, W.G., Guo, C.J., Zhang, X.M., Cheng, Z., Zhang, S.Z., Li, D.M., Li, W.B., and Zhang, D.Y. (2016). Temporal and spatial expression of phenylalanine ammonia-lyase gene family in soybean. Crops, 57\u201362."},{"key":"ref_24","first-page":"97","article-title":"Comparison of phenylalanine ammonia-lyase activity in Populus trichocarpa and preparation of cinnamic acid","volume":"44","author":"Zhang","year":"2020","journal-title":"J. Nanjing For. Univ. (Nat. Sci. Ed.)"},{"key":"ref_25","first-page":"1","article-title":"Genome-wide identification and expression pattern analysis of the PAL gene family in Carya cathayensis","volume":"42","author":"Liu","year":"2025","journal-title":"J. Zhejiang A&F Univ."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Liu, H.X., and Li, B. (2025). Genome-Wide Identification of the PAL Gene Family in Camellia nitidissima and Functional Characterization of CnPAL1 Gene by In Vitro Expression. Genes, 16.","DOI":"10.3390\/genes16111251"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1038\/nature08670","article-title":"Genome sequence of the palaeopolyploid soybean","volume":"463","author":"Schmutz","year":"2010","journal-title":"Nature"},{"key":"ref_28","first-page":"1742","article-title":"Response of Stylosanthes guianensis phenylalanine ammonia-lyase (SgPALs) to biotic and abiotic stresses","volume":"40","author":"Guo","year":"2019","journal-title":"Chin. J. Trop. Crops"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/j.plaphy.2020.09.030","article-title":"Characterisation, Expression and Functional Analysis of PAL Gene Family in Cephalotaxus Hainanensis","volume":"156","author":"He","year":"2020","journal-title":"Plant Physiol. Biochem."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.tplants.2019.09.011","article-title":"Plant Phenylalanine\/Tyrosine Ammonia-Lyases","volume":"25","author":"Barros","year":"2020","journal-title":"Trends Plant Sci."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Yang, Q., He, Z.Q., Zheng, C.J., He, R.Y., Chen, Y., Zhuo, R.Y., and Qiu, W.M. (2025). Genome-wide identification and comprehensive analysis of the GARP transcription factor superfamily in Populus deltoides. Genes, 16.","DOI":"10.3390\/genes16030322"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Karamat, U., Guo, J., Jiang, S., Khan, I., Lu, M., Fu, M., and Li, G. (2024). Comprehensive, Genome-Wide Identification and Expression Analyses of Phenylalanine Ammonia-Lyase Family under Abiotic Stresses in Brassica Oleracea. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms251910276"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Zhou, H., Liu, H., Ma, J., Yue, M., Wang, Y., Zhao, P., and Chen, Z. (2025). Genome-Wide Identification, Transcriptome Dynamics, and Expression Regulation of the Key Lignin Biosynthesis Gene Families PAL and CAD in Black Walnut Shell. BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-06884-1"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Wang, T., Zheng, Y., Sun, L., Guan, M., Hu, Y., Yu, H., Wu, D., and Du, J. (2025). Analysis of Maize PAL Pan Gene Family and Expression Pattern under Lepidopteran Insect Stress. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1651563"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Fernandes, P., Pimentel, D., Ramiro, R.S., Silva, M.d.C., Fevereiro, P., and Costa, R.L. (2024). Dual transcriptomic analysis reveals early induced Castanea defense-related genes and Phytophthora cinnamomi effectors. Front. Plant Sci., 15.","DOI":"10.3389\/fpls.2024.1439380"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"141255","DOI":"10.1016\/j.ijbiomac.2025.141255","article-title":"PcMYB44 regulated host resistance to Botryosphaeria dothidea through activation of lignin biosynthesis and disease-resistance gene expression in pear","volume":"306","author":"Lv","year":"2025","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"uhae359","DOI":"10.1093\/hr\/uhae359","article-title":"The long non-coding RNA MSTRG.32189-PcmiR399b-PcUBC24 module regulates phosphate accumulation and disease resistance to Botryosphaeria dothidea in pear","volume":"12","author":"Yang","year":"2025","journal-title":"Hortic. Res."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"10111","DOI":"10.1038\/s41598-019-46635-5","article-title":"Fungal canker pathogens trigger carbon starvation by inhibiting carbon metabolism in poplar stems","volume":"9","author":"Li","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"101523","DOI":"10.1016\/j.pmpp.2020.101523","article-title":"Fungal pathogens of canker disease trigger canopy dieback in poplar saplings by inducing functional failure of the phloem and cambium and carbon starvation in the xylem","volume":"112","author":"Xing","year":"2020","journal-title":"Physiol. Mol. Plant Pathol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e2300275","DOI":"10.1002\/biot.202300275","article-title":"Engineering Phenylalanine Ammonia Lyase to Limit Feedback Inhibition by Cinnamate and Enhance Biotransformation","volume":"19","author":"Pavale","year":"2024","journal-title":"Biotechnol. J."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1104\/pp.114.249136","article-title":"Down-Regulation of Kelch Domain-Containing F-Box Protein in Arabidopsis Enhances the Production of (Poly)Phenols and Tolerance to Ultraviolet Radiation","volume":"167","author":"Zhang","year":"2015","journal-title":"Plant Physiol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"4994","DOI":"10.1105\/tpc.113.119644","article-title":"Arabidopsis Kelch Repeat F-Box Proteins Regulate Phenylpropanoid Biosynthesis via Controlling the Turnover of Phenylalanine Ammonia-Lyase","volume":"25","author":"Zhang","year":"2013","journal-title":"Plant Cell"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"eadz6970","DOI":"10.1126\/sciadv.adz6970","article-title":"A Dual Role of Arabidopsis PAL Nuclear Localization in Fine Tuning Flavonoid Biosynthesis","volume":"12","author":"Sun","year":"2026","journal-title":"Sci. Adv."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"113909","DOI":"10.1016\/j.celrep.2024.113909","article-title":"The Idesia polycarpa genome provides insights into its evolution and oil biosynthesis","volume":"43","author":"Zuo","year":"2024","journal-title":"Cell Rep."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/17\/7842\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T08:57:22Z","timestamp":1788339442000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/17\/7842"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,2]]},"references-count":47,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ijms27177842"],"URL":"https:\/\/doi.org\/10.3390\/ijms27177842","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,2]]}}}