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

文献类型： 外文期刊

第一作者： Yang, Yinqing

作者： Yang, Yinqing;Li, Ying;Hou, Xilin;Yang, Yinqing;Zhang, Lei;Tang, Qi;Zhang, Lingkui;Li, Xing;Chen, Shumin;Zhang, Kang;Cheng, Feng

作者机构：

关键词： Brassica oleracea; Oxford nanopore technologies; Gene annotation; Alternative splicing

期刊名称：HORTICULTURAL PLANT JOURNAL （ 影响因子：5.7； 五年影响因子：5.5 ）

ISSN： 2095-9885

年卷期： 2024 年 10 卷 4 期

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收录情况： SCI

摘要： 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.

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