Homoeologous evolution of the allotetraploid genome of Poa annua L.
Homoeologous evolution of the allotetraploid genome of Poa annua L.
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DOI：
10.1186/s12864-023-09456-5
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发表时间：
2023-06-26
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影响因子：
4.4
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中科院分区：
文献类型：
--
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一年生早熟禾是一种异源四倍体草坪草，是一种重要的农艺杂草，也是地球上分布最广的植物之一。在这里，我们报道了青杨的二倍体祖先P.infima和P.Supina的染色体规模的基因组组装，并使用跨越这三个物种的多组学分析来更好地理解P.annua的进化新颖性。我们发现，二倍体在550万-630万年前偏离了他们共同的祖先，并在5万年前杂交形成了P.annua ≤ 。二倍体基因组在染色体结构上相似，最显著的区别是其转座元件的进化历史不同，导致基因组大小的差异为1.7 × 。在异源四倍体青杨中，我们发现反转录转座子从较大的(A)亚基因组到较小的(B)亚基因组的偏向移动。结果表明，青海对虾的B亚组优先积累基因，其基因表达水平较高。对另外几个青杨种质的全基因组测序显示了大规模的染色体重排，其特征是大范围的TE缩小，并有证据支持基因组平衡假说。二倍体祖先的分化进化在赋予青杨显着的表型可塑性方面起到了中心作用。我们发现，植物基因(由选择和漂移引导)和转座元件(主要由寄主免疫引导)以独特的方式对多倍体做出反应，而青杨利用全基因组复制来清除高度寄生的异色序列。本文提供的发现和基因组资源将使开发用于加速杂草科学和草坪育种的同源特异性标记成为可能。网上版载有补充材料，可在10.1186/s12864-023-09456-5查阅。
Poa annua (annual bluegrass) is an allotetraploid turfgrass, an agronomically significant weed, and one of the most widely dispersed plant species on earth. Here, we report the chromosome-scale genome assemblies of P. annua’s diploid progenitors, P. infirma and P. supina, and use multi-omic analyses spanning all three species to better understand P. annua’s evolutionary novelty. We find that the diploids diverged from their common ancestor 5.5 – 6.3 million years ago and hybridized to form P. annua ≤ 50,000 years ago. The diploid genomes are similar in chromosome structure and most notably distinguished by the divergent evolutionary histories of their transposable elements, leading to a 1.7 × difference in genome size. In allotetraploid P. annua, we find biased movement of retrotransposons from the larger (A) subgenome to the smaller (B) subgenome. We show that P. annua’s B subgenome is preferentially accumulating genes and that its genes are more highly expressed. Whole-genome resequencing of several additional P. annua accessions revealed large-scale chromosomal rearrangements characterized by extensive TE-downsizing and evidence to support the Genome Balance Hypothesis. The divergent evolutions of the diploid progenitors played a central role in conferring onto P. annua its remarkable phenotypic plasticity. We find that plant genes (guided by selection and drift) and transposable elements (mostly guided by host immunity) each respond to polyploidy in unique ways and that P. annua uses whole-genome duplication to purge highly parasitized heterochromatic sequences. The findings and genomic resources presented here will enable the development of homoeolog-specific markers for accelerated weed science and turfgrass breeding. The online version contains supplementary material available at 10.1186/s12864-023-09456-5.
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影响因子：
48
作者：
Cheng H;Concepcion GT;Feng X;Zhang H;Li H
通讯作者：
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影响因子：
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影响因子：
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