基因组分化后环境响应基因的偏差保留。

IF 11 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Marc Beringer, Rimjhim Roy Choudhury, Terezie Mandáková, Sandra Grünig, Manuel Poretti, Ilia J Leitch, Martin A Lysak, Christian Parisod
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引用次数: 0

摘要

全基因组复制(WGD)循环以及随后通过亚基因组分化造成的基因丢失的分子基础和后果在很大程度上仍然难以捉摸。据推测,转座元件等内源驱动因素可形成全基因组优势和偏向分化,导致保守的最小分化(LF)和退化的最大分化(MF)亚基因组。相比之下,外源因素(如环境压力诱导的因素)的作用却被忽视了。本文对大约 1100 万年前经历过 WGD 事件的高山龅牙芥(Biscutella laevigata; Brassicaceae)进行了染色体组尺度的组装,并结合了对热、冷、干旱和食草动物的转录反应,以评估基因表达如何与 MF 和 LF 亚基因组的不同基因保留相关联。转座元件减少了附近基因在中频亚基因组中的表达和保留,而剂量平衡则抵消了转座元件的影响,在纯化选择下,剂量平衡是保留重复基因产物的主要内源促进因子。与 "把爱好变成工作 "的模式一致,大约三分之一的环境响应型重复基因表现出了新的表达模式,其中一个拷贝通常保持条件表达,而另一个拷贝则进化出了组成型表达,这突出表明外源因素是基因保留的主要驱动力。该中多倍体基因组显示出不均衡的分化模式,一些区域保持无偏性,而另一些区域则显示出高偏性和环境响应基因的显著富集。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Biased Retention of Environment-Responsive Genes Following Genome Fractionation.

The molecular underpinnings and consequences of cycles of whole-genome duplication (WGD) and subsequent gene loss through subgenome fractionation remain largely elusive. Endogenous drivers, such as transposable elements (TEs), have been postulated to shape genome-wide dominance and biased fractionation, leading to a conserved least-fractionated (LF) subgenome and a degenerated most-fractionated (MF) subgenome. In contrast, the role of exogenous factors, such as those induced by environmental stresses, has been overlooked. In this study, a chromosome-scale assembly of the alpine buckler mustard (Biscutella laevigata; Brassicaceae) that underwent a WGD event about 11 million years ago is coupled with transcriptional responses to heat, cold, drought, and herbivory to assess how gene expression is associated with differential gene retention across the MF and LF subgenomes. Counteracting the impact of TEs in reducing the expression and retention of nearby genes across the MF subgenome, dosage balance is highlighted as a main endogenous promoter of the retention of duplicated gene products under purifying selection. Consistent with the "turn a hobby into a job" model, about one-third of environment-responsive duplicates exhibit novel expression patterns, with one copy typically remaining conditionally expressed, whereas the other copy has evolved constitutive expression, highlighting exogenous factors as a major driver of gene retention. Showing uneven patterns of fractionation, with regions remaining unbiased, but with others showing high bias and significant enrichment in environment-responsive genes, this mesopolyploid genome presents evolutionary signatures consistent with an interplay of endogenous and exogenous factors having driven gene content following WGD-fractionation cycles.

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来源期刊
Molecular biology and evolution
Molecular biology and evolution 生物-进化生物学
CiteScore
19.70
自引率
3.70%
发文量
257
审稿时长
1 months
期刊介绍: Molecular Biology and Evolution Journal Overview: Publishes research at the interface of molecular (including genomics) and evolutionary biology Considers manuscripts containing patterns, processes, and predictions at all levels of organization: population, taxonomic, functional, and phenotypic Interested in fundamental discoveries, new and improved methods, resources, technologies, and theories advancing evolutionary research Publishes balanced reviews of recent developments in genome evolution and forward-looking perspectives suggesting future directions in molecular evolution applications.
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