Genome-wide analysis of alternative splicing divergences between Brassica hexaploid and its parents
Genome-wide analysis of alternative splicing divergences between Brassica hexaploid and its parents
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芸苔属六倍体及其亲本之间选择性剪接差异的全基因组分析
DOI：
10.1007/s00425-019-03198-z
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发表时间：
2019-08-01
期刊：
影响因子：
4.3
通讯作者：
Wang, Jianbo
中科院分区：
文献类型：
--
作者：
Wang, Ruihua;Liu, Helian;Wang, Jianbo
与亲本相比，芸苔属六倍体发生了显著的AS变化，这可能提供了多样化的基因表达调控模式，增强了芸苔属六倍体在进化过程中的适应性。选择性剪接（alternative splicing，AS）在植物生长发育过程中的多种生物学过程中起着重要作用。为探讨异源多倍体化对基因AS模式的影响，利用RNA-seq技术对芸苔属六倍体及其亲本进行了全基因组AS分析。总共，我们发现7913（27540 AS事件），14447（70179 AS事件），和13205（60804 AS事件）AS基因在芜菁，埃塞俄比亚芥，和芸苔属六倍体，分别。在芸苔属六倍体中共发现了920个新的AS基因。芸苔属六倍体与亲本间存在56个不同的剪接基因。此外，在芸苔属六倍体中，大多数5 ′可变剪接位点位于显性5 ′可变剪接位点上游4 bp处，大多数3 ′可变剪接位点位于显性3 ′可变剪接位点下游3bp处，与B相似。carinata。此外，我们克隆并测序了GRP 7/8的RT-PCR产物的所有扩增子，即Bol 045859，Bol 016025和Bol 02880。这三个基因被发现以一种新的方式产生AS转录本。芸苔属六倍体及其亲本间AS基因的表达模式存在差异，包括AS事件的丢失和获得。异源多倍体化改变了芸苔属六倍体前体mRNA的选择性剪接位点，从而导致转录本序列发生改变。本研究为异源多倍体植物基因的AS模式提供了新的认识，为多倍体适应性的研究提供了参考。
Compared with its parents, Brassica hexaploid underwent significant AS changes, which may provide diversified gene expression regulation patterns and could enhance its adaptability during evolution Polyploidization is considered a significant evolution force that promotes species formation. Alternative splicing (AS) plays a crucial role in multiple biological processes during plant growth and development. To explore the effects of allopolyploidization on the AS patterns of genes, a genome-wide AS analysis was performed by RNA-seq in Brassica hexaploid and its parents. In total, we found 7913 (27540 AS events), 14447 (70179 AS events), and 13205 (60804 AS events) AS genes in Brassica rapa, Brassica carinata, and Brassica hexaploid, respectively. A total of 920 new AS genes were discovered in Brassica hexaploid. There were 56 differently spliced genes between Brassica hexaploid and its parents. In addition, most of the alternative 5ʹ splice sites were located 4 bp upstream of the dominant 5ʹ splice sites, and most of the alternative 3ʹ splice sites were located 3 bp downstream of the dominant 3ʹ splice sites in Brassica hexapliod, which was similar to B. carinata. Furthermore, we cloned and sequenced all amplicons from the RT-PCR products of GRP7/8, namely, Bol045859, Bol016025 and Bol02880. The three genes were found to produce AS transcripts in a new way. The AS patterns of genes were diverse between Brassica hexaploid and its parents, including the loss and gain of AS events. Allopolyploidization changed alternative splicing sites of pre-mRNAs in Brassica hexaploid, which brought about alterations in the sequences of transcripts. Our study provided novel insights into the AS patterns of genes in allopolyploid plants, which may provide a reference for the study of polyploidy adaptability.