首页|Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing

Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing

扫码查看
原文链接
  • NETL
  • NSTL
  • 万方数据
Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so on.The genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of B.oleracea,has been widely used as a common reference in biological research.Although its genome assembly has been updated twice,the current gene annotation still lacks information on untranslated regions(UTRs)and alternative splicing(AS).Here,we constructed a high-quality gene annotation(JZSv3)using a full-length transcriptome acquired by nanopore sequencing,yielding a total of 59 452 genes and 75 684 transcripts.Additionally,we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference,and found that 3843 out of 11 908 differentially expressed genes(DEGs)underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold stress.Meanwhile,we also identified many AS genes,including BolLHCB5 and BolHSP70,that displayed distinct expression patterns within variant transcripts of the same gene,highlighting the importance of JZSv3 as a pivotal reference for AS analysis.Overall,JZSv3 provides a valuable resource for exploring gene function,especially for obtaining a deeper understanding of AS regulation mechanisms.

Brassica oleraceaOxford nanopore technologiesGene annotationAlternative splicing

Yinqing Yang、Lei Zhang、Qi Tang、Lingkui Zhang、Xing Li、Shumin Chen、Kang Zhang、Ying Li、Xilin Hou、Feng Cheng

展开 >

State Key Laboratory of Crop Genetics and Germplasm Enhancement,College of Horticulture,Nanjing Agricultural University,Nanjing 210095,China

State Key Laboratory of Vegetable Biobreeding,Institute of Vegetables and Flowers,Chinese Academy of Agricultural Sciences,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs,Sino-Dutch Joint Laboratory of Horticultural Genomics,Beijing 100081,China

National Natural Science Foundation of ChinaNational Natural Science Foundation of ChinaNational Natural Science Foundation of ChinaCentral Publicinterest Scientific Institution Basal Research FundInnovation Program of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops,Ministry of Agriculture and Rural Affairs,P.R.ChinaNIFADepartment of Agriculture,via UC-Berkeley,USA

319724113172204831630068Y2022PT23

2024

10.1016/j.hpj.2024.03.005

园艺学报(英文版)

园艺学报(英文版)

CSTPCD
ISSN：
年,卷(期)：2024.10(4)
  • 1