PDF(Pubmed)
Abstract：
Brachypodium grass species have been selected as model plants for functional genomics of grass crops, and to elucidate the origins of allopolyploidy and perenniality in monocots, due to their small genome sizes and feasibility of cultivation. However, genome sizes differ greatly between diploid or polyploid Brachypodium lineages. We have used genome skimming sequencing data to uncover the composition, abundance, and phylogenetic value of repetitive elements in 44 representatives of the major Brachypodium lineages and cytotypes. We also aimed to test the possible mechanisms and consequences of the \"polyploid genome shock hypothesis\" (PGSH) under three different evolutionary scenarios of variation in repeats and genome sizes of Brachypodium allopolyploids. Our data indicated that the proportion of the genome covered by the repeatome in the Brachypodium species showed a 3.3-fold difference between the highest content of B. mexicanum-4x (67.97%) and the lowest of B. stacei-2x (20.77%), and that changes in the sizes of their genomes were a consequence of gains or losses in their repeat elements. LTR-Retand and Tekay retrotransposons were the most frequent repeat elements in the Brachypodium genomes, while Ogre retrotransposons were found exclusively in B. mexicanum. The repeatome phylogenetic network showed a high topological congruence with plastome and nuclear rDNA and transcriptome trees, differentiating the ancestral outcore lineages from the recently evolved core-perennial lineages. The 5S rDNA graph topologies had a strong match with the ploidy levels and nature of the subgenomes of the Brachypodium polyploids. The core-perennial B. sylvaticum presents a large repeatome and characteristics of a potential post-polyploid diploidized origin. Our study evidenced that expansions and contractions in the repeatome were responsible for the three contrasting responses to the PGSH. The exacerbated genome expansion of the ancestral allotetraploid B. mexicanum was a consequence of chromosome-wide proliferation of TEs and not of WGD, the additive repeatome pattern of young allotetraploid B. hybridum of stabilized post-WGD genome evolution, and the genomecontraction of recent core-perennials polyploids (B. pinnatum, B. phoenicoides) of repeat losses through recombination of these highly hybridizing lineages. Our analyses have contributed to unraveling the evolution of the repeatome and the genome size variation in model Brachypodium grasses.
摘要：
短枝草种已被选为草类作物功能基因组学的模型植物，并阐明单子叶植物中异源多倍体和多年性的起源，由于它们的基因组尺寸小和培养的可行性。然而,二倍体或多倍体Brachypodium谱系之间的基因组大小差异很大。我们已经使用基因组略读测序数据来揭示成分，丰度,和44个主要的Brachypodium谱系和细胞类型代表中重复元素的系统发育值。我们还旨在测试“多倍体基因组休克假说”（PGSH）在Brachypodium异源多倍体重复和基因组大小变异的三种不同进化情景下的可能机制和后果。我们的数据表明，在Brachypodium物种中，重复组覆盖的基因组比例在墨西哥芽孢杆菌4x的最高含量（67.97％）和最低的B.stacei-2x（20.77％）之间显示出3.3倍的差异，基因组大小的变化是重复元素得失的结果。LTR-Retand和Tekay逆转录转座子是Brachypodium基因组中最常见的重复元件，而食人魔反转录转座子只在墨西哥芽孢杆菌中发现。重复组系统发育网络显示出与质体和核rDNA以及转录组树的高度拓扑一致性，将祖先的外核谱系与最近进化的核心多年生谱系区分开来。5SrDNA图拓扑与Brachypodium多倍体的倍性水平和亚基因组的性质具有很强的匹配性。核心多年生B.sylvaticum具有很大的重复性和潜在的多倍体后二倍体起源的特征。我们的研究证明，重复组中的扩张和收缩是对PGSH的三种相反反应的原因。祖先异源四倍体墨西哥芽孢杆菌的基因组扩展加剧是TEs而不是WGD的全染色体增殖的结果，稳定后WGD基因组进化的年轻异源四倍体杂种芽孢杆菌的加性重复序列模式，和最近多年生核心多倍体的基因组学(B.pinnatum,phoenicoides）通过重组这些高度杂交的谱系而重复丢失。我们的分析有助于揭示Brachypodium草模型中重复组的进化和基因组大小变化。
