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基因家族的数量及结构变异是物种适应自然变化的重要机制。深入研究猪(Sus scrofa)的基因家族进化，可以了解其基因扩张和收缩事件，从而揭示猪在进化过程中为适应环境而发生改变的特殊机制。本研究采用比较基因组学方法，对猪、牛(Bos taurus)、绵羊(Ovis aries)、羊驼(Vicugna pacos)、鸡(Gallus gallus)和小鼠(Mus musculus)的参考基因组进行比较，以鉴定猪基因家族。利用PAML软件计算物种分化时间，并通过CAFE软件分析猪基因家族中的扩张和收缩基因。将鉴定到的显著收缩和扩张基因注释到KEGG、 GO、 KOG数据库中进行通路分析。结果表明，猪共有16 749个基因家族，包含20 660个基因。同其他5个物种相比，猪具有55个特有的基因家族，包含470个基因。基因家族收缩与扩张分析结果表明，猪基因组中共有334个基因家族发生收缩，214个基因家族发生扩张。其中，有110个基因家族的扩张显著，包含473个基因；152个基因家族的收缩显著，包含102个基因。富集结果表明，显著扩张家族基因主要富集在生殖过程、胆汁分泌和化学致癌作用DNA加合物等方面；显著收缩家族基因主要富集在系统性红斑狼疮、酒精中毒、坏死性肺炎以及冠状病毒病等方面；猪特有基因家族的基因主要富集在脂肪转运代谢、嗅觉受体活性、气味剂结合以及脂肪酸的降解等方面。本研究鉴定和分析了猪显著收缩与扩张及其特有的基因家族，并发现其在多个生物过程中具有重要的功能。这些结果有助于更深入了解猪的适应性进化，并为其作为生物模型研究人类疾病提供了新的线索。
Abstract：The number and structural variation of gene families are crucial mechanisms for species to adapt to natural changes. In-depth study of the evolution of pig(Sus scrofa) gene families can reveal the special mechanisms by which pigs change to adapt to their environment, by identifying expansion and contraction events. In this study, comparative genomics was used to compare the reference genomes of pigs, cattle(Bos taurus), sheep(Ovis aries), alpacas(Vicugna pacos), chickens(Gallus gallus), and mouse(Mus musculus)to identify pig gene families. The PAML software was used to calculate the species differentiation time, and the CAFF software was used to analyze the expansion and contraction genes in pig gene families. The identified significant contraction and expansion genes were enriched in the KEGG, GO, and KOG databases for pathway analysis. Results showed that pigs had 16 749 gene families, containing 20 660 genes. Compared to the other 5 species, pigs had 55 unique gene families containing 470 genes. The analysis of gene family contraction and expansion revealed that the pig genome had 334 gene families that underwent contraction, and 214 gene families underwent expansion, including 110 gene families with significant expansion containing 473 genes, and 152 gene families with significant contraction containing 102 genes. The enrichment results showed that the genes of significantly expanded families were mainly enriched in reproductive processes, bile secretion, chemical carcinogen-DNA adducts and so on. The genes of significantly contracted families were mainly enriched in systemic lupus erythematosus, alcohol poisoning, necrotizing pneumonia, coronavirus disease and so on. The genes of pig-specific gene families were mainly enriched in fat transport metabolism, olfactory receptor activity, odorant binding, fatty acid degradation and so on. In conclusion, this study identified and analyzed significant contraction and expansion and unique gene families in pigs and found that they had important functions in multiple biological processes. These results help to further understand the adaptive evolution of pigs and provide new clues for using pigs as a biological model to study human diseases.
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基本信息:
DOI：10.13417/j.gab.042.000726
中图分类号:S828
引用信息:
[1]袁巍,毕欢,张雨丹,等.基于比较基因组分析猪特有基因家族及其进化[J].基因组学与应用生物学,2023,42(07):726-735.DOI:10.13417/j.gab.042.000726.
基金信息:
贵州省科技计划项目(黔科合支撑[2022]一般087); 贵州大学引进人才科研项目(贵大人基合字[2019]34号); 贵州省优秀青年科技人才培养计划(黔科合平台人才[2021]5630号); 贵州省生猪产业发展项目(2021)共同资助
2023-06-09
2023-06-09
2023-06-09