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植物假基因的结构特征和复制模式。

Structural characterization and duplication modes of pseudogenes in plants.

机构信息

Department of Agricultural, Food, and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.

Dipartimento di Agraria, Università degli studi di Sassari, Via Enrico de Nicola 1, 07100, Sassari, Italy.

出版信息

Sci Rep. 2021 Mar 5;11(1):5292. doi: 10.1038/s41598-021-84778-6.

DOI:10.1038/s41598-021-84778-6
PMID:33674668
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7935947/
Abstract

We identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa and Phaseolus vulgaris) and one monocot (Oryza sativa). Retroposition was considered of modest importance for pseudogene formation in all investigated species except V. vinifera, which showed an unusually high number of retro-pseudogenes in non coding genic regions. By using a pipeline for the classification of sequence duplicates in plant genomes, we compared the relative importance of whole genome, tandem, proximal, transposed and dispersed duplication modes in the pseudo and functional gene complements. Pseudogenes showed higher tendencies than functional genes to genomic dispersion. Dispersed pseudogenes were prevalently fragmented and showed high sequence divergence at flanking regions. On the contrary, those deriving from whole genome duplication were proportionally less than expected based on observations on functional loci and showed higher levels of flanking sequence conservation than dispersed pseudogenes. Pseudogenes deriving from tandem and proximal duplications were in excess compared to functional loci, probably reflecting the high evolutionary rate associated with these duplication modes in plant genomes. These data are compatible with high rates of sequence turnover at neutral sites and double strand break repairs mediated duplication mechanisms.

摘要

我们鉴定和描述了五个植物物种的假基因补充

四个双子叶植物（拟南芥、葡萄、杨属和菜豆）和一个单子叶植物（水稻）。除了葡萄，反转录在所有被调查的物种中对于假基因形成的作用都被认为是适度的，葡萄在非编码基因区域显示出异常高数量的反转录假基因。通过使用植物基因组中序列重复分类的流水线，我们比较了全基因组、串联、近端、转座和分散重复模式在假基因和功能基因补充中的相对重要性。假基因比功能基因更倾向于基因组分散。分散的假基因普遍碎片化，并在侧翼区域显示出高的序列差异。相反，那些来自全基因组复制的假基因比例低于基于功能基因座观察到的预期，并且比分散的假基因显示出更高水平的侧翼序列保守性。来自串联和近端重复的假基因数量超过了功能基因座，可能反映了与植物基因组中这些重复模式相关的高进化率。这些数据与中性位点的高序列周转率和双链断裂修复介导的复制机制是一致的。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/5b12eb23bd9e/41598_2021_84778_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/65d2bda9f0af/41598_2021_84778_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/44b495d4b2a5/41598_2021_84778_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/03c45473678d/41598_2021_84778_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/a923b7113786/41598_2021_84778_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/213a45c6f31f/41598_2021_84778_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/f719e92aa6ab/41598_2021_84778_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/8016832dd7b9/41598_2021_84778_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/5b12eb23bd9e/41598_2021_84778_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/65d2bda9f0af/41598_2021_84778_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/44b495d4b2a5/41598_2021_84778_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/03c45473678d/41598_2021_84778_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/a923b7113786/41598_2021_84778_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/213a45c6f31f/41598_2021_84778_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/f719e92aa6ab/41598_2021_84778_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/8016832dd7b9/41598_2021_84778_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/812c/7935947/5b12eb23bd9e/41598_2021_84778_Fig8_HTML.jpg

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