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Extent, speed, and causes of changes in the protein-coding gene repertoire of holometabolous insects (Insecta: Endopterygota)

全变态昆虫（昆虫纲：内翅目）蛋白质编码基因库变化的程度、速度和原因

基本信息

批准号：
315489364
负责人：
Professor Dr. Bernhard Misof, Ph.D.
金额：
--
依托单位：
Leibniz-Institut zur Analyse des Biodiversitätswandels (LIB)
依托单位国家：
德国
项目类别：
Research Grants
财政年份：
2016
资助国家：
德国
起止时间：
2015-12-31 至 2017-12-31
项目状态：
已结题

来源：
https://gepris.dfg.de/gepris/projekt/315489364?language=en
关键词：
Extent speed causes changes protein

项目摘要

Most phenotypic differences between species are the manifestation of differences between genomes. While the evolution of organismic diversity is often interpreted as evolution of regulatory networks, changes in the species' gene repertoire could also have significantly contributed to the evolution of this diversity. In fact, genome sequencing projects have led to the unexpected insight that, in eukaryotes, virtually every species harbors a rich set of seemingly species-specific protein-coding genes. This result implies that gene turnover (GT) could be an underrated factor in the evolution of organismic diversity. However, robust inference of GT rates and identification of genomic factors and mechanisms that cause GT rate changes require a dense and representative sampling of sequenced genomes as well as knowledge of the phylogenetic relationships and divergence times of the respective species. Such data sets have been sparse, which hampered examining the role of GT in the genomes of insects, arguably the most diverse lineage of animals (given their phylogenetic age). To obtain a better understanding of GT as an important and general aspect of genome dynamics, we invested into compiling comprehensive genomic and phylogenetic data, which form the basis for the research project outlined here. Specifically, we de novo sequenced the genomes of 33 insect species, representing almost all major lineages of holometabolous insects, and inferred a robust insect backbone tree of life including reliable divergence time estimates. Exploiting this unique set of data, we will estimate GT rates in insect genomes and assess the most promising genomic factors that could cause GT rate changes: non-homologous (ectopic) recombination mediated by the presence and propagation of transposable elements (TEs) and whole genome duplication (WGD). To infer the historic occurrence of these events, we will determine the repertoires and diversification histories of protein-coding genes and TEs and search for genome-wide simultaneous expansions of gene families. Finally, we will assess whether changes in TE abundance and/or WGD correlate with GT rate changes. The outcome of our proposed study will shed new light on the dynamics of GT rates in insect genomes and on mechanisms and factors that likely cause them. Since the gene repertoire is a fundamental property of an organism's genome, our results will be of major interest for researchers in various research fields, ranging from evolutionary biology and comparative genomics to developmental biology and biodiversity research.

物种之间的大多数表型差异是基因组之间差异的表现。虽然器官多样性的进化通常被解释为调控网络的进化，但物种基因库的变化也可能对这种多样性的进化做出了重大贡献。事实上，基因组测序项目已经导致了意想不到的洞察力，在真核生物中，几乎每个物种都拥有一套丰富的看似物种特异性的蛋白质编码基因。这一结果表明，基因周转（GT）可能是一个被低估的因素在进化的器官多样性。然而，强大的推断GT率和鉴定基因组因素和机制，导致GT率的变化需要一个密集的和有代表性的采样测序基因组以及知识的系统发育关系和分歧时间的各个物种。这样的数据集是稀疏的，这阻碍了研究GT在昆虫基因组中的作用，可以说昆虫是最多样化的动物谱系（考虑到它们的系统发育年龄）。为了更好地了解GT作为基因组动态的一个重要和一般方面，我们投资编译了全面的基因组和系统发育数据，这些数据构成了这里概述的研究项目的基础。具体来说，我们从头测序的33种昆虫的基因组，几乎所有的主要谱系的全变态昆虫，并推断出一个强大的昆虫骨干树的生活，包括可靠的分歧时间估计。利用这组独特的数据，我们将估计昆虫基因组中的GT率，并评估可能导致GT率变化的最有前途的基因组因素：由转座因子（TE）和全基因组复制（WGD）的存在和传播介导的非同源（异位）重组。为了推断这些事件的历史发生，我们将确定蛋白质编码基因和TE的剧目和多样化的历史，并寻找基因家族的全基因组同时扩增。最后，我们将评估TE丰度和/或WGD的变化是否与GT速率变化相关。我们提出的研究结果将为昆虫基因组中GT速率的动态以及可能导致它们的机制和因素提供新的见解。由于基因库是一个生物体的基因组的基本属性，我们的研究结果将主要兴趣的研究人员在各个研究领域，从进化生物学和比较基因组学发育生物学和生物多样性研究。