GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes

doi:10.1101/gr.238733.118

CORC > 数学与系统科学研究院 > 中国科学院数学与系统科学研究院 > 应用数学研究所

	GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
	Shao, Yi 4,5,6; Chen, Chunyan 4,5,6; Shen, Hao 7; He, Bin Z.3,8,9; Yu, Daqi 4,5,6; Jiang, Shuai 10,11; Zhao, Shilei 6,12; Gao, Zhiqiang 6,13; Zhu, Zhenglin 14; Chen, Xi 15,16
刊名	GENOME RESEARCH
	2019-04-01
卷号	29 期号:4 页码:682-696
ISSN号	1088-9051
DOI	10.1101/gr.238733.118
英文摘要	The origination of new genes contributes to phenotypic evolution in humans. Two major challenges in the study of new genes are the inference of gene ages and annotation of their protein-coding potential. To tackle these challenges, we created GenTree, an integrated online database that compiles age inferences from three major methods together with functional genomic data for new genes. Genome-wide comparison of the age inference methods revealed that the synteny-based pipeline (SBP) is most suited for recently duplicated genes, whereas the protein-family-based methods are useful for ancient genes. For SBP-dated primate-specific protein-coding genes (PSGs), we performed manual evaluation based on published PSG lists and showed that SBP generated a conservative data set of PSGs by masking less reliable syntenic regions. After assessing the coding potential based on evolutionary constraint and peptide evidence from proteomic data, we curated a list of 254 PSGs with different levels of protein evidence. This list also includes 41 candidate misannotated pseudogenes that encode primate-specific short proteins. Coexpression analysis showed that PSGs are preferentially recruited into organs with rapidly evolving pathways such as spermatogenesis, immune response, mother-fetus interaction, and brain development. For brain development, primate-specific KRAB zinc-finger proteins (KZNFs) are specifically up-regulated in the mid-fetal stage, which may have contributed to the evolution of this critical stage. Altogether, hundreds of PSGs are either recruited to processes under strong selection pressure or to processes supporting an evolving novel organ.
资助项目	Strategic Priority Research Program of the Chinese Academy of Sciences[XDB13000000] ; National Key Basic Research Program of China[2015CB943001] ; National Key Basic Research Program of China[2013CB531202] ; National Natural Science Foundation of China[91731302] ; National Natural Science Foundation of China[31771410] ; National Natural Science Foundation of China[31200941] ; National Natural Science Foundation of China[31500668] ; Fundamental Research Funds for the Central Universities[106112016CDJXY290002] ; HPC Platform of BIG ; NCMIS CAS ; HPC Platform of the Scientific Information Centre of IOZ
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
语种	英语
出版者	COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
WOS记录号	WOS:000462858600015
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/34321]
专题	应用数学研究所
通讯作者	Zhang, Yong E.
作者单位	1.Chinese Acad Sci, CAS Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China 2.Univ Chicago, Dept Ecol & Evolut, 940 E 57Th St, Chicago, IL 60637 USA 3.Univ Iowa, Dept Biol, Iowa City, IA 52242 USA 4.Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China 5.Chinese Acad Sci, State Key Lab Integrated Management Pest Insects, Inst Zool, Beijing 100101, Peoples R China 6.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 7.Hunan Univ Technol, Coll Comp, Zhuzhou 412007, Hunan, Peoples R China 8.Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA 9.Harvard Univ, Howard Hughes Med Inst, Cambridge, MA 02138 USA 10.Peking Univ, Ctr Bioinformat, Sch Life Sci, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China
推荐引用方式 GB/T 7714	Shao, Yi,Chen, Chunyan,Shen, Hao,et al. GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes[J]. GENOME RESEARCH,2019,29(4):682-696.
APA	Shao, Yi.,Chen, Chunyan.,Shen, Hao.,He, Bin Z..,Yu, Daqi.,...&Zhang, Yong E..(2019).GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes.GENOME RESEARCH,29(4),682-696.
MLA	Shao, Yi,et al."GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes".GENOME RESEARCH 29.4(2019):682-696.