UMR85 Physiologie de la Reproduction et des Comportements, INRA, Nouzilly, France UMR7247, CNRS, Nouzilly, France Université François Rabelais de Tours, Tours, France Institut Français du Cheval et de l'Equitation, Nouzilly, France.
UMR1388 INRA/INPT ENSAT/INPT ENVT, Génétique, Physiologie et Systèmes d'élevage, INRA, Castanet Tolosan, France.
Mol Biol Evol. 2014 Oct;31(10):2637-46. doi: 10.1093/molbev/msu208. Epub 2014 Jul 10.
Gene loss is one of the main drivers in the evolution of genomes and species. The demonstration that a gene has been lost by pseudogenization is truly complete when one finds the pseudogene in the orthologous genomic region with respect to active genes in other species. In some cases, the identification of such orthologous loci is not possible because of chromosomal rearrangements or if the gene of interest has not yet been sequenced. This question is particularly important in the case of birds because the genomes of avian species possess only about 15,000 predicted genes, in comparison with 20,000 in mammals. Yet, gene loss raises the question of which functions are affected by the changes in gene counts. We describe a systematic approach that makes it possible to demonstrate gene loss in the chicken genome even if a pseudogene has not been found. By using phylogenetic and synteny analysis in vertebrates, genome-wide comparisons between the chicken genome and expressed sequence tags, RNAseq data analysis, statistical analysis of the chicken genome, and radiation hybrid mapping, we show that resistin, TNFα, and PAI-1 (SERPINE1), three genes encoding adipokines inhibiting insulin sensitivity, have been lost in chicken and zebra finch genomes. Moreover, omentin, a gene encoding an adipokine that enhances insulin sensitivity, has also been lost in the chicken genome. Overall, only one adipokine inhibiting insulin sensitivity and five adipokines enhancing insulin sensitivity are still present in the chicken genome. These genetic differences between mammals and chicken, given the functions of the genes in mammals, would have dramatic consequences on chicken endocrinology, leading to novel equilibriums especially in the regulation of energy metabolism, insulin sensitivity, as well as appetite and reproduction.
基因丢失是基因组和物种进化的主要驱动力之一。当在与其他物种中活性基因相对应的同源基因组区域中发现假基因时，表明一个基因已经通过假基因化而丢失，这才是真正完整的证明。在某些情况下，由于染色体重排或感兴趣的基因尚未测序，无法识别此类同源基因座。在鸟类的情况下，这个问题尤为重要，因为鸟类物种的基因组仅包含约 15000 个预测基因，而哺乳动物的基因组则包含 20000 个基因。然而，基因丢失引发了一个问题，即哪些功能受到基因数量变化的影响。我们描述了一种系统的方法，即使没有发现假基因，也可以证明鸡基因组中的基因丢失。通过在脊椎动物中进行系统发育和同线性分析、鸡基因组与表达序列标签之间的全基因组比较、RNAseq 数据分析、鸡基因组的统计分析以及辐射杂交作图，我们表明，抵抗素、TNFα 和 PAI-1（SERPINE1）这三个编码抑制胰岛素敏感性的脂肪因子的基因在鸡和斑胸草雀基因组中丢失了。此外，编码增强胰岛素敏感性的脂肪因子的基因 omentin 也在鸡基因组中丢失了。总的来说，只有一种抑制胰岛素敏感性的脂肪因子和五种增强胰岛素敏感性的脂肪因子仍然存在于鸡基因组中。这些哺乳动物和鸡之间的遗传差异，考虑到这些基因在哺乳动物中的功能，将对鸡的内分泌学产生巨大影响，导致特别是在能量代谢、胰岛素敏感性以及食欲和生殖的调节方面出现新的平衡。
