Deciphering the Diploid Ancestral Genome of the Mesohexaploid Brassica rapa
Deciphering the Diploid Ancestral Genome of the Mesohexaploid Brassica rapa
复制标题
DOI：
10.1105/tpc.113.110486
复制
发表时间：
2013-05-01
期刊：
影响因子：
11.6
通讯作者：
Wang, Xiaowu
中科院分区：
文献类型：
--
作者：
Cheng, Feng;Mandakova, Terezie;Wang, Xiaowu
油菜属包括几种重要的农业和园艺作物。它们目前的基因组结构是通过全基因组三倍化和广泛的二倍化形成的。几个十字花科植物基因组序列的获得，特别是大白菜基因组序列的获得，使得研究中观六倍体甘蓝基因组从其二倍体祖先进化成为可能。我们通过将油菜的全基因组序列与十字花科植物祖先基因组和现存的十字花科植物基因组进行比较，构建了油菜的三个祖先亚基因组(n=10)。这三个油菜古基因组明显由7条染色体组成，类似于祖先易位原金龟亚科的核型(tPCK；n=7)，后者是原金龟亚科的进化较年轻的变体(n=7)。基于对甘蓝、黑甘蓝、萝卜等近缘物种基因组序列或连锁图谱的比较分析，我们提出了将三个tPCK类基因组分两步合并，形成具有42条染色体的Brassiceae族的六倍体祖先。Brassiceae随后的多样化以广泛的基因组重组和易位事件介导的染色体数量减少为标志，随后是着丝粒的丢失和/或失活。此外，通过种间基因组比较，我们细化了祖先十字花科植物核型(n=8)的7个基因组块的间隔，从而修订了十字花科植物进化基因组学的关键参考基因组。
The genus Brassica includes several important agricultural and horticultural crops. Their current genome structures were shaped by whole-genome triplication followed by extensive diploidization. The availability of several crucifer genome sequences, especially that of Chinese cabbage (Brassica rapa), enables study of the evolution of the mesohexaploid Brassica genomes from their diploid progenitors. We reconstructed three ancestral subgenomes of B. rapa (n = 10) by comparing its whole-genome sequence to ancestral and extant Brassicaceae genomes. All three B. rapa paleogenomes apparently consisted of seven chromosomes, similar to the ancestral translocation Proto-Calepineae Karyotype (tPCK; n = 7), which is the evolutionarily younger variant of the Proto-Calepineae Karyotype (n = 7). Based on comparative analysis of genome sequences or linkage maps of Brassica oleracea, Brassica nigra, radish (Raphanus sativus), and other closely related species, we propose a two-step merging of three tPCK-like genomes to form the hexaploid ancestor of the tribe Brassiceae with 42 chromosomes. Subsequent diversification of the Brassiceae was marked by extensive genome reshuffling and chromosome number reduction mediated by translocation events and followed by loss and/or inactivation of centromeres. Furthermore, via interspecies genome comparison, we refined intervals for seven of the genomic blocks of the Ancestral Crucifer Karyotype (n = 8), thus revising the key reference genome for evolutionary genomics of crucifers.