Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds
Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds
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DOI：
10.1093/molbev/msx236
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发表时间：
2017-12-01
影响因子：
10.7
通讯作者：
Galtier, Nicolas
中科院分区：
文献类型：
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作者：
Botero-Castro, Fidel;Figuet, Emeric;Galtier, Nicolas
根据目前的组合，鸟类基因组与其他羊膜动物谱系的不同之处在于：1)含有较少的基因；2)表现出高稳定性的核型和重组图谱；3)进化速度(dN/ds)与生活史特征之间没有任何关联，不像哺乳动物和非鸟类爬行动物。我们质疑鸟类缺失基因的真实性，并调查鸟类基因内容的不充分表现是否可能对先前的进化分析产生了偏见。挖掘RNAseq数据，我们发现鸟类基因组组合中缺失的绝大多数基因实际上存在于大多数鸟类中。这些主要对应于鸟类基因组中富含GC的部分，这是最难测序、组装和注释的部分。随着这些基因被纳入高质量比对的系统基因组分析中，我们发现非同义与同义替换率(dN/ds)与新鸟类生活史特征之间存在显著的正相关关系。我们报道了GC偏向的基因转换在鸟类中对dN/ds比率的强烈影响，以及古陆鸟(鸵鸟和同类)和Galloanserae(鸡、鸭和同类)的特殊行为。鸟类基因组包含的基因并不比哺乳动物或非鸟类爬行动物少。以前的分析忽略了类似于15%的鸟类基因互补。GC富集区是羊膜动物基因组的关键组成部分，也是最难进入的区域。它们经历了特殊的分子过程，必须包括在内，以便在鸟类中进行无偏见的功能和比较基因组分析。
According to current assemblies, avian genomes differ from those of the other lineages of amniotes in 1) containing a lower number of genes; 2) displaying a high stability of karyotype and recombination map; and 3) lacking any correlation between evolutionary rates (dN/dS) and life-history traits, unlike mammals and nonavian reptiles. We question the reality of the bird missing genes and investigate whether insufficient representation of bird gene content might have biased previous evolutionary analyses. Mining RNAseq data, we show that the vast majority of the genes missing from avian genome assemblies are actually present in most species of birds. These mainly correspond to the GC-rich fraction of the bird genome, which is the most difficult to sequence, assemble and annotate. With the inclusion of these genes in a phylogenomic analysis of high-quality alignments, we uncover a positive and significant correlation between the ratio of nonsynonymous to synonymous substitution rate (dN/dS) and life-history traits in Neoaves. We report a strong effect of GC-biased gene conversion on the dN/dS ratio in birds and a peculiar behavior of Palaeognathae (ostrich and allies) and Galloanserae (chickens, ducks and allies). Avian genomes do not contain fewer genes than mammals or nonavian reptiles. Previous analyses have overlooked similar to 15% of the bird gene complement. GC-rich regions, which are the most difficult to access, are a key component of amniote genomes. They experience peculiar molecular processes and must be included for unbiased functional and comparative genomic analyses in birds.