Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi. Apteryx mantelli mantelli

Background To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli) and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold. Results Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes. Conclusions The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available.

研究背景 为解析棕几维鸟（Apteryx australis mantelli）核编码蛋白基因的分子进化模式，并确定鸟类演化的时间尺度，我们采用下一代测序技术对几维鸟胚胎的转录组进行了测序。随后以鸡蛋白质组作为组装支架，对保守蛋白编码区域完成组装。
研究结果 我们利用1543个保守蛋白编码基因，估算得到几维鸟与鸡之间的中性进化分歧率约为45%，这一数值与利用相同基因集计算得到的人-鼠进化分歧率大致相当。我们发现大量基因处于较强的选择约束之下，且多数表达基因均参与发育基因调控过程。本研究揭示了基因表达水平与蛋白质进化之间存在显著关联。我们通过覆盖700余个核基因的序列数据，估算得到两个基底鸟类支系——古颚总目（Palaeognathae）和新颚总目（Neognathae）之间的分歧时间为1.32亿年，这与此前基于线粒体基因开展的相关研究结果一致。
研究结论 本研究结果揭示了鸟类保守蛋白编码区域的突变模式与纯化选择特征。此外，本研究提出了一种成本相对可控的方法，可用于窥探基因组的核心分子进化属性，尤其适用于暂无近缘基因组序列可供参考的研究场景。