Downing Tim, Cormican Paul, O'Farrelly Cliona, Bradley Daniel G, Lloyd Andrew T
Smurfit Institute of Genetics, Trinity College, University of Dublin, Ireland.
BMC Res Notes. 2009 Dec 15;2:254. doi: 10.1186/1756-0500-2-254.
The basis for understanding the characteristics of gene functional categories in chicken has been enhanced by the ongoing sequencing of the zebra finch genome, the second bird species to be extensively sequenced. This sequence provides an avian context for examining how variation in chicken has evolved since its divergence from its common ancestor with zebra finch as well as well as a calibrating point for studying intraspecific diversity within chicken. Immune genes have been subject to many selective processes during their evolutionary history: this gene class was investigated here in a set of orthologous chicken and zebra finch genes with functions assigned from the human ortholog. Tests demonstrated that nonsynonymous sites at immune genes were highly conserved both in chicken and on the avian lineage. McDonald-Kreitman tests provided evidence of adaptive evolution and a higher rate of selection on fixation of nonsynonymous substitutions at immune genes compared to that at non-immune genes. Further analyses showed that GC content was much higher in chicken than in zebra finch genes, and was significantly elevated in both species' immune genes. Pathogen challenges are likely to have driven the selective forces that have shaped variation at chicken immune genes, and continue to restrict diversity in this functional class.
斑胸草雀基因组的持续测序增强了我们对鸡基因功能类别的特征的理解基础，斑胸草雀是第二种被广泛测序的鸟类。该序列为研究鸡自与斑胸草雀的共同祖先分化以来的变异如何进化提供了鸟类背景，同时也为研究鸡种内多样性提供了一个校准点。免疫基因在其进化历史中经历了许多选择过程：在此，我们在一组直系同源的鸡和斑胸草雀基因中研究了这一基因类别，这些基因的功能是根据人类直系同源基因确定的。测试表明，免疫基因的非同义位点在鸡和鸟类谱系中都高度保守。麦克唐纳-克里特曼测试提供了适应性进化的证据，并且与非免疫基因相比，免疫基因在固定非同义替换时的选择率更高。进一步分析表明，鸡基因中的GC含量远高于斑胸草雀基因，并且在两个物种的免疫基因中均显著升高。病原体挑战可能推动了塑造鸡免疫基因变异的选择力量，并继续限制这一功能类别的多样性。
