The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
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DOI：
10.1111/tpj.13801
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发表时间：
2018-02-01
期刊：
影响因子：
7.2
通讯作者：
Rensing, Stefan A.
中科院分区：
文献类型：
--
作者：
Lang, Daniel;Ullrich, Kristian K.;Rensing, Stefan A.
苔藓模型Physcomitrella patens的基因组草图由大约2000个无序支架组成。为了能够分析基因组结构和进化，我们使用遗传连锁和(完)长DNA片段的测序产生了染色体规模的基因组组合。我们发现57%的基因组包含转座元件(TES)，其中一些可能在生命周期中活跃地转座。与开花植物基因组不同，富含基因和TE的区域在染色体上总体上分布均匀。然而，染色体是单着丝点的，一类Copia元件的峰可能与着丝粒重合。5.7%的蛋白质编码基因存在明显的基因体甲基化，这通常与低GC和低表达相一致。一些巨型病毒的插入在转录上是活跃的，可能通过siRNA介导的沉默来保护配子免受病毒感染。基于结构的检测方法表明，基因组是通过两轮全基因组复制(WGD)进化的，这显然在苔藓中很常见，但在地钱和角菜中并不常见。数百个基因存在于自植物的最后一个共同祖先以来一直保守的共线区域。这些共线区域丰富了与植物特有的细胞生长和组织组织相关的功能。P.patens基因组缺乏大多数开花植物基因组所特有的富含TE的着丝粒周围和富含基因的远端区域。需要更多的非种子植物基因组来解开植物基因组的进化，并了解P.patens的基因组结构是苔藓还是苔藓的典型。
The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene-and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.