Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.
Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.
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DOI：
10.1111/j.1365-294x.2009.04487.x
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发表时间：
2010-03
影响因子：
4.9
通讯作者：
Ellegren H
中科院分区：
文献类型：
--
作者：
Künstner A;Wolf JB;Backström N;Whitney O;Balakrishnan CN;Day L;Edwards SV;Janes DE;Schlinger BA;Wilson RK;Jarvis ED;Warren WC;Ellegren H
下一代测序技术提供了一种有吸引力的手段来获取比较基因组分析所需的大规模序列数据。为了分析整个鸟类基因组的突变率变异和选择强度模式，我们使用 Roche 454 技术对 10 种不同的非模型鸟类进行了脑转录组测序。来自从头组装的重叠群与两种可用的鸟类参考基因组（鸡和斑胸草雀）进行比对。总的来说，我们在所有 10 个物种中鉴定出了 6499 个不同的基因，每个物种的每次完整运行中发现了约 1000 个基因。我们发现了 Z 染色体突变率高于常染色体（男性偏向突变）的证据，并且中性替代率 (dS) 与染色体大小之间呈负相关。对跨染色体基因的平均 dN/dS 比率 (ω) 的分析支持希尔-罗伯逊效应（连锁位点的选择效应），并指出 ω 作为选择的独立衡量标准的随机问题。总体而言，这项研究证明了下一代测序对于获取基因组资源以进行非模式生物的比较基因组分析的有用性。
Next-generation sequencing technology provides an attractive means to obtain large-scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with ~1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (dS) and chromosome size. Analyses of the mean dN/dS ratio (ω) of genes across chromosomes supported the Hill–Robertson effect (the effect of selection at linked loci) and point at stochastic problems with ω as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.