三倍化复制对白菜花粉特异表达候选基因的影响

doi:10.3864/j.issn.0578-1752.2015.18.016

摘要/Abstract

摘要： 【目的】研究三倍化复制事件后白菜花粉特异表达候选基因的进化情况，为研究白菜的花粉特异表达基因提供理论依据。【方法】利用SynOrths软件及拟南芥花粉特异表达基因集，通过共线性分析获取白菜中的花粉特异表达候选基因。通过InterproScan获取这些候选基因的GO注释，并将这些GO注释划分到与花粉相关的13个大类。然后统计每个GO的基因数占不同拷贝类型基因总数的比例，对不同拷贝类型间进行比较。进一步根据白菜3个亚基因组集，将这些候选基因划分到不同的亚基因组上。通过分析白菜花粉特异表达候选基因中串联重复基因与拟南芥基因的共线性关系，推测这些串联重复基因是在芸薹属特有的三倍化事件之前形成，还是在其之后形成。【结果】通过对拟南芥中的1 651个花粉特异表达基因进行共线性分析，在白菜中总共找到了1 962个花粉特异表达候选基因。拟南芥特异基因集里有182个串联重复基因，而白菜包含了137个串联重复基因。白菜与拟南芥在花粉特异表达基因数目上没有明显差异，因此推测这些基因的大部分拷贝可能在三倍化复制事件后发生了丢失。549个拟南芥花粉特异表达基因在白菜上找不到相应的共线性基因，白菜在进化过程中可能丢失掉了这部分基因。拟南芥花粉特异表达基因中有898个串联重复基因在白菜中对应单或多拷贝的非串联重复基因。在白菜中对应单拷贝基因的拟南芥基因数目为480个，而且所占比例高达53.5%。另外，322个基因在白菜中对应两拷贝，比例约为35.8%。而在白菜中对应三拷贝的拟南芥基因只有96个，大约占总数目的10.7%。在白菜中，单拷贝和两拷贝的基因数目显著高于三拷贝，这说明三倍化后白菜中大部分花粉特异候选基因发生了丢失，部分两拷贝和三拷贝的基因也可能处于进化选择的过程中。白菜三拷贝基因功能在7个GO分类上的比例高于单拷贝和两拷贝，而白菜两拷贝在所有GO分类上都有分布。白菜花粉特异候选基因中的大部分串联重复基因可能在三倍化事件以后发生了基因丢失，变成了非串联重复基因。也有部分非串联重复基因在三倍化事件之后形成了串联重复基因。【结论】白菜花粉特异候选基因在芸薹属特有的三倍化事件之后处于进化之中，并且三倍化事件可能促进了3种拷贝类型基因的功能差异。

关键词: 白菜, 花粉特异表达, 三倍化复制, 共线性, 进化

Abstract: 【Objective】 The objective of this study is to research the evolution of the candidate genes of pollen specific expression in Brassica rapa after whole-genome triplication (WGT). This study will provide a theoretical basis for pollen specific expressed genes in B. rapa in the future research. 【Method】 The genes of pollen specific expression in B. rapa were acquired by SynOrths referred to Arabidopsis thaliana based on their syntenic relationship. InterproScan was used to get their Gene Ontology (GO), which were grouped into 13 categories related to pollen. To compare among three duplicated categories, the ratio of gene number of each GO to total number of genes in these categories was counted. Furthermore, these genes were grouped into three subgenomes based on their explicit dataset of B. rapa genes. Based on the syntenic relationship of tandem genes of pollen specific expression in B. rapa with genes in A. thaliana，whether these genes were generated before WGT or after the event was determined. 【Result】 Totally, 1962 candidate genes of pollen specific expression in B. rapa were verified via the syntenic relationship with 1651 genes in A. thaliana. There are 182 tandem genes in A. thaliana, while 137 tandem genes in B. rapa. The result showed that the number of pollen specific expressed genes between A. thaliana and B. rapa was almost equivalent, so it could be inferred that most of copy genes of B. rapa were lost after WGT event occurs. A total of 549 genes of pollen specific expression in A. thaliana were not found syntenic counterparts in B. rapa, so these genes might be also lost after WGT. There are 898 genes of pollen specific expression in A. thaliana corresponding to these genes with single-copy, double-copies or triple-copies in B. rapa. A total of 480 genes in A. thaliana with single-copy in B. rapa, accounting for 53.5%, which is the largest proportion. While 322 genes with double-copies account for about 35.8%, and only 96 genes with triple-copies account for 10.7%. The candidate genes of pollen specific expression with triple-copies in all three subgenomes of B. rapa were more than the other two copy classifies on seven functional categories, while the function of these genes with double-copies were dispersed into all functional categories. Most of tandem genes of pollen specific expression were turned into non-tandem genes, but some non-tandem genes of pollen specific expression developed into tandem genes in B. rapa after WGT. 【Conclusion】 These results indicated that the candidate genes of pollen specific expression had an ongoing evolution after WGT, and the WGT event may contribute to the functional difference existed in three classifies of copy genes in B. rapa.

Key words: Brassica rapa, pollen specific expression, whole-genome triplication, synteny, evolution

王晓波，马原，程锋，武剑，梁建丽，王晓武. 三倍化复制对白菜花粉特异表达候选基因的影响[J]. 中国农业科学, 2015, 48(18): 3727-3732.

WANG Xiao-bo, MA Yuan, CHENG Feng, WU Jian, LIANG Jian-li, WANG Xiao-wu. The Influence of Whole-Genome Triplication (WGT) on the Candidate Genes of Pollen Specific Expression in Brassica rapa[J]. Scientia Agricultura Sinica, 2015, 48(18): 3727-3732.

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