A Phylogenetic Analysis of Chloroplast Genomes Elucidates the Relationships of the Six Economically Important Brassica Species Comprising the Triangle of U.
A Phylogenetic Analysis of Chloroplast Genomes Elucidates the Relationships of the Six Economically Important Brassica Species Comprising the Triangle of U.
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DOI：
10.3389/fpls.2017.00111
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发表时间：
2017
影响因子：
5.6
通讯作者：
Borm TJ
中科院分区：
文献类型：
--
作者：
Li P;Zhang S;Li F;Zhang S;Zhang H;Wang X;Sun R;Bonnema G;Borm TJ
芸苔属包括许多世界范围内具有重要经济意义的栽培作物。成熟的甘蓝属模型，即 U 三角，由通过种间杂交产生的三种基本二倍体植物物种（白菜、甘蓝和黑甘蓝）和三种双二倍体物种（甘蓝型油菜、芥菜和甘蓝）组成。尽管因其商业相关性而被广泛研究，但芸苔属物种起源的几个方面以及这六个物种内部和之间的关系仍然存在悬而未决的问题。在这里，我们成功地从头组装了所有六个物种的芸苔属基因型的 60 个完整叶绿体基因组。生成了不同芸苔属植物叶绿体基因组中单核苷酸变异以及插入和缺失的完整图谱。叶绿体基因组由两个反向重复之间的大单拷贝（LSC 和 SSC）区域组成，虽然叶绿体基因组的这些区域具有非常不同的分子进化速率，但不同区域的系统发育分析没有产生矛盾的拓扑结构，并将芸苔属分为四个进化枝。 B. carinata 和 B. juncea 分别与其杂交供体 B. nigra 和 B. rapa 共享叶绿体基因组，这符合 U 模型。令人惊讶的是，白菜菜显示出两种叶绿体基因组的证据，其中一种类型是某些意大利西兰花品种所特有的。甘蓝型油菜显然有两个独立杂交事件的证据，因为它含有甘蓝型油菜叶绿体基因组。分歧估计表明，B. nigra 和 B. carinata 在 1370 万年前 (Mya) 与主要的芸苔属分支分化，而 B. rapa 和 B. oleracea 在 2.18 Mya 分歧。完整叶绿体 DNA 序列的使用不仅为比较基因组分析提供了见解，而且为更好地理解芸苔属内的系统发育关系铺平了道路。
The Brassica genus comprises many economically important worldwide cultivated crops. The well-established model of the Brassica genus, U’s triangle, consists of three basic diploid plant species (Brassica rapa, Brassica oleracea, and Brassica nigra) and three amphidiploid species (Brassica napus, Brassica juncea, and Brassica carinata) that arose through interspecific hybridizations. Despite being extensively studied because of its commercial relevance, several aspects of the origin of the Brassica species and the relationships within and among these six species still remain open questions. Here, we successfully de novo assembled 60 complete chloroplast genomes of Brassica genotypes of all six species. A complete map of the single nucleotide variants and insertions and deletions in the chloroplast genomes of different Brassica species was produced. The chloroplast genome consists of a Large and a Small Single Copy (LSC and SSC) region between two inverted repeats, and while these regions of chloroplast genomes have very different molecular evolutionary rates, phylogenetic analyses of different regions yielded no contradicting topologies and separated the Brassica genus into four clades. B. carinata and B. juncea share their chloroplast genome with one of their hybridization donors B. nigra and B. rapa, respectively, which fits the U model. B. rapa, surprisingly, shows evidence of two types of chloroplast genomes, with one type specific to some Italian broccoletto accessions. B. napus clearly has evidence for two independent hybridization events, as it contains either B. rapa chloroplast genomes. The divergence estimation suggests that B. nigra and B. carinata diverged from the main Brassica clade 13.7 million years ago (Mya), while B. rapa and B. oleracea diverged at 2.18 Mya. The use of the complete chloroplast DNA sequence not only provides insights into comparative genome analysis but also paves the way for a better understanding of the phylogenetic relationships within the Brassica genus.