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Age distribution patterns of human gene families: divergent for Gene Ontology categories and concordant between different subcellular localizations

文献类型： 外文期刊

作者： Liu, Gangbiao 1 ; Zou, Yangyun 1 ; Cheng, Qiqun 3 ; Zeng, Yanwu 4 ; Gu, Xun 2 ; Su, Zhixi 1 ;

作者机构： 1.Fudan Univ, State Key Lab Genet Engn, Shanghai 200433, Peoples R China

2.Fudan Univ, Sch Life Sci, MOE, Key Lab Contemporary Anthropol, Shanghai 200433, Peoples R China

3.Chinese Acad Fishery Sci, East China Sea Fisheries Res Inst, Shanghai 200090, Peoples R China

4.Shanghai Jiao Tong Univ, Inst Med Sci, Shanghai Stem Cell Inst, Shanghai 200025, Peoples R China

5.Iowa State Univ, Dept Genet Dev & Cell Biol GDCB, Ames, IA 50011 USA

关键词： Gene duplication;Duplication age;Gene retention;Copy number variants;Genome duplication

期刊名称：MOLECULAR GENETICS AND GENOMICS （ 影响因子：3.291； 五年影响因子：3.257 ）

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收录情况： SCI

摘要： The age distribution of gene duplication events within the human genome exhibits two waves of duplications along with an ancient component. However, because of functional constraint differences, genes in different functional categories might show dissimilar retention patterns after duplication. It is known that genes in some functional categories are highly duplicated in the early stage of vertebrate evolution. However, the correlations of the age distribution pattern of gene duplication between the different functional categories are still unknown. To investigate this issue, we developed a robust pipeline to date the gene duplication events in the human genome. We successfully estimated about three-quarters of the duplication events within the human genome, along with the age distribution pattern in each Gene Ontology (GO) slim category. We found that some GO slim categories show different distribution patterns when compared to the whole genome. Further hierarchical clustering of the GO slim functional categories enabled grouping into two main clusters. We found that human genes located in the duplicated copy number variant regions, whose duplicate genes have not been fixed in the human population, were mainly enriched in the groups with a high proportion of recently duplicated genes. Moreover, we used a phylogenetic tree-based method to date the age of duplications in three signaling-related gene superfamilies: transcription factors, protein kinases and G-protein coupled receptors. These superfamilies were expressed in different subcellular localizations. They showed a similar age distribution as the signaling-related GO slim categories. We also compared the differences between the age distributions of gene duplications in multiple subcellular localizations. We found that the distribution patterns of the major subcellular localizations were similar to that of the whole genome. This study revealed the whole picture of the evolution patterns of gene functional categories in the human genome.

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