大白菜抗根肿病的全长转录组和可变剪切的综合分析

doi:10.1016/j.jia.2022.09.014

摘要/Abstract

摘要：

十字花科芸薹属根肿病是由芸薹根肿菌（Plasmodiophora brassicae）侵染引起的世界范围内普遍发生的一种重要土传病害，在全世界多个国家均有分布。以往对大白菜抗根肿病基因的研究主要采用转录组测序技术，不能提供准确的转录本组装和结构信息。本研究采用PacBio RS II SMRT测序技术，获得了大白菜抗根肿病DH40R接菌0、2、5、8、13和22天混合根的全长转录组。总的来说，从SMRT测序数据中发现了39,376个高质量转录本和26,270个开放阅读框。此外，还鉴定出426个注释的长链非编码RNA、56个转录因子家族、1883个具有poly(A)位点的基因和1691个可变剪切事件。另外，其中有1202个基因在DH40R中至少有一个AS事件。与以往的RNA-seq数据比较显示，6个差异表达的AS基因（1个抗病，5个防御反应）可能参与了根肿病抗性防御。

Abstract:

Chinese cabbage is an economically important Brassica vegetable worldwide, and clubroot, which is caused by the soil-borne protist plant pathogen Plasmodiophora brassicae is regarded as a destructive disease to Brassica crops. Previous studies on the gene transcripts related to Chinese cabbage resistance to clubroot mainly employed RNA-seq technology, although it cannot provide accurate transcript assembly and structural information. In this study, PacBio RS II SMRT sequencing was used to generate full-length transcriptomes of mixed roots at 0, 2, 5, 8, 13, and 22 days after P. brassicae infection in the clubroot-resistant line DH40R. Overall, 39 376 high-quality isoforms and 26 270 open reading frames (ORFs) were identified from the SMRT sequencing data. Additionally, 426 annotated long noncoding RNAs (lncRNAs), 56 transcription factor (TF) families, 1 883 genes with poly(A) sites and 1 691 alternative splicing (AS) events were identified. Furthermore, 1 201 of the genes had at least one AS event in DH40R. A comparison with RNA-seq data revealed six differentially expressed AS genes (one for disease resistance and five for defensive response) that are potentially involved in P. brassicae resistance. The results of this study provide valuable resources for basic research on clubroot resistance in Chinese cabbage.

Key words: Chinese cabbage , clubroot , full-length transcriptome , SMRT sequencing , alternative splicing

SU He-nan, YUAN Yu-xiang, YANG Shuang-juan, WEI Xiao-chun, ZHAO Yan-yan, WANG Zhi-yong, QIN Liu-yue, YANG Zhi-yuan, NIU Liu-jing, LI Lin, ZHANG Xiao-wei. 大白菜抗根肿病的全长转录组和可变剪切的综合分析[J]. Journal of Integrative Agriculture, 2023, 22(11): 3284-3295.

SU He-nan, YUAN Yu-xiang, YANG Shuang-juan, WEI Xiao-chun, ZHAO Yan-yan, WANG Zhi-yong, QIN Liu-yue, YANG Zhi-yuan, NIU Liu-jing, LI Lin, ZHANG Xiao-wei. Comprehensive analysis of the full-length transcripts and alternative splicing involved in clubroot resistance in Chinese cabbage[J]. Journal of Integrative Agriculture, 2023, 22(11): 3284-3295.

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