十字花科植物叶绿体基因组结构及变异分析

Chloroplast Genome Structure and Variation Analysis of Brassicaceae Species

该研究比较了十字花科22个属22个物种的叶绿体基因组,以揭示十字花科叶绿体基因组的一般特征和变异特征。结果发现:(1)基因组大小为150kb左右,不同植物的叶绿体基因组之间存在1~5kb的差异,基因组大小的差异主要是大单拷贝(LSC)长度的差异引起的。(2)十字花科物种基因顺序基本一致,未检测到基因的重排和倒置事件。(3)trnY、trnG、ycf15、rps16基因在一些物种中发生丢失,petB、petD内含子序列也在个别物种内丢失。(4)基因组的4个边界相对保守,反向重复区a-大单拷贝区(IRa-LSC)边界处于rps19基因上,反向重复区a-小单拷贝区(IRa-SSC)边界在所有物种中均位于ycf1基因中,但是rps19和ycf1在边界两侧的长度具有差异,反向重复区b-小单拷贝区(IRb-SSC)边界在大部分物种中位于ycf1假基因和ndhF基因的重叠区内,而在庭荠(Alyssum desertorum)、小花南芥(Arabis alpina)2个物种中发生了改变,分别位于ycf1假基因和ndhF基因内。(5)29个蛋白编码基因长度发生变化,基因长度的变异来源于基因内含子或者编码区长度的改变,ycf1基因长度在3个物种中发生了大片段的缺失,部分基因长度的变化具有明显的系统发育信号。(6)基于叶绿体基因组数据构建的系统发育树具有较好的分辨率,各个进化分支具有较高的支持率。研究结果表明,利用叶绿体基因组数据可以为解决进化较快、系统发育分辨率低的植物类群的系统分类和系统发育关系提供更有力的证据。

In this study, chloroplast genomes of 22 species belonging to 22 genera were compared to reveal the general characteristics and structural variation of chloroplast genome of Brassicaceae.The results showed that：（1） the genome size was about 150 kb, and there were 1-5 kb differences among the chloroplast genomes of different plants.The differences in genome size were mainly caused by the difference of LSC length.（2） The gene order of Brassicaceae species was basically the same, no gene rearrangement and inversion event was found.（3） trnY, trnG, ycf15, rps16 genes were lost in some species, petB, petD intron sequences were also lost in individual species.（4） The four boundaries of the genome was relatively conservative, IRa-LSC boundary located in the rps19 gene, the IRa-SSC boundary located in the ycf1 gene in all species, but the length of rps19 and ycf1 was different on each side of the boundary in different species.The IRb-SSC boundary located in the overlap area of the ycf1 and ndhF genes in most species, whereas this boundary changed in Alyssum desertorum and Arabis alpina, lied in ycf1 pseudogene and ndhF genes, respectively.（5） Gene length of 29 protein-coding genes varied among the 22 cp genomes, and the variation was from the differences of intron or the coding sequence.Large fragment deletions were observed of ycf1 gene in the three species.The length of some genes revealed obvious phylogenetic signals.（6） The phylogenetic tree of Brassicaceae which was constructed based on the cp genome data had good resolution, and the evolutionary branched were of high supports.The results of this study showed that the cp genome can provide more evidence for the systematics and phylogeny of plant groups that are with faster evolution and low phylogenetic resolution.