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

doi:10.1101/gr.238733.118

CSpace > 应用数学研究所

	GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
	Shao, Yi 1,2,3; Chen, Chunyan 1,2,3; Shen, Hao 4; He, Bin Z.5,6,16; Yu, Daqi 1,2,3; Jiang, Shuai 7,8; Zhao, Shilei 3,9; Gao, Zhiqiang 3,10; Zhu, Zhenglin 11; Chen, Xi 12,13; Fu, Yan3,10 ; Chen, Hua 3,9,14; Gao, Ge 7,8; Long, Manyuan 15; Zhang, Yong E.1,2,3,14
	2019-04-01
发表期刊	GENOME RESEARCH
ISSN	1088-9051
卷号	29 期号:4 页码:682-696
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.
DOI	10.1101/gr.238733.118
语种	英语
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
WOS类目	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:000462858600015
出版者	COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/34322
专题	应用数学研究所
通讯作者	Zhang, Yong E.
作者单位	1.Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China 2.Chinese Acad Sci, State Key Lab Integrated Management Pest Insects, Inst Zool, Beijing 100101, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Hunan Univ Technol, Coll Comp, Zhuzhou 412007, Hunan, Peoples R China 5.Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA 6.Harvard Univ, Howard Hughes Med Inst, Cambridge, MA 02138 USA 7.Peking Univ, Ctr Bioinformat, Sch Life Sci, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China 8.Peking Univ, Beijing Adv Innovat Ctr Genom ICG, Biomed Pioneering Innovat Ctr BIOPIC, Beijing 100871, Peoples R China 9.Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genom & Precis Med, Beijing 100101, Peoples R China 10.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Key Lab Random Complex Struct & Data Sci, Beijing 100190, Peoples R China 11.Chongqing Univ, Sch Life Sci, Chongqing 400044, Peoples R China 12.Wuhan Inst Biotechnol, Wuhan 430072, Hubei, Peoples R China 13.Wuhan Univ, Med Res Inst, Wuhan 430072, Hubei, Peoples R China 14.Chinese Acad Sci, CAS Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China 15.Univ Chicago, Dept Ecol & Evolut, 940 E 57Th St, Chicago, IL 60637 USA 16.Univ Iowa, Dept Biol, Iowa City, IA 52242 USA
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.