Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden.
Mol Ecol. 2010 Mar;19 Suppl 1(Suppl 1):266-76. doi: 10.1111/j.1365-294X.2009.04487.x.
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 approximately 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 (d(S)) and chromosome size. Analyses of the mean d(N)/d(S) ratio (omega) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with omega 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.
下一代测序技术为比较基因组分析提供了获取大规模序列数据的有吸引力的手段。为了分析鸟类基因组中突变率变化和选择强度的模式，我们使用罗氏 454 技术对 10 种不同的非模式鸟类物种进行了脑转录组测序。从头组装的 contigs 被映射到两个现有的鸟类参考基因组，鸡和斑胸草雀。总共，我们在所有 10 个物种中鉴定了 6499 个不同的基因，每个物种的每个完整运行中大约有 1000 个基因。我们发现 Z 染色体的突变率高于常染色体（雄性偏性突变），并且中性替换率（d(S)）与染色体大小之间呈负相关。对跨染色体的基因平均 d(N)/d(S)比值（ω）的分析支持了 Hill-Robertson 效应（连锁位点的选择效应），并指出作为选择的独立衡量标准，ω 存在随机问题。总的来说，这项研究表明，下一代测序技术在获取非模式生物比较基因组分析的基因组资源方面是有用的。
