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

物种间的大多数表型差异是基因组差异的表现。虽然生物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似乎是物种特异性的蛋白质编码基因。这一结果表明，基因转换（GT）在生物多样性进化中可能是一个被低估的因素。然而，要对GT率进行可靠的推断，并确定导致GT率变化的基因组因素和机制，需要密集和有代表性的测序基因组样本，以及对各自物种的系统发育关系和分化时间的了解。这样的数据集一直很稀少，这阻碍了对昆虫基因组中GT的作用的研究，昆虫可以说是最多样化的动物谱系（考虑到它们的系统发育年龄）。为了更好地理解GT是基因组动力学的一个重要而普遍的方面，我们投入了大量资金，汇编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，我们对33种昆虫的基因组进行了重新测序，这些昆虫几乎代表了全代谢昆虫的所有主要谱系，并推断了一个强大的昆虫骨干生命树，包括可靠的分化时间估计。利用这组独特的数据，我们将估计昆虫基因组中的GT率，并评估最有可能导致GT率变化的基因组因素：由转座因子（te）的存在和繁殖介导的非同源（异位）重组和全基因组重复（WGD）。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的谱库和多样化历史，并寻找基因家族的全基因组同步扩增。最后，我们将评估TE丰度和/或WGD的变化是否与GT率变化相关。我们提出的研究结果将揭示昆虫基因组中GT率的动态以及可能导致GT率的机制和因素。由于基因库是生物体基因组的基本属性，我们的研究结果将引起各个研究领域的研究人员的主要兴趣，从进化生物学和比较基因组学到发育生物学和生物多样性研究。

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.