Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics

doi:10.1186/s12862-015-0345-x

	Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics
	Zhao, Yi ; Tang, Liang ; Li, Zhe 1; Jin, Jinpu ; Luo, Jingchu ; Gao, Ge
	2015
发表期刊	BMC EVOLUTIONARY BIOLOGY
ISSN	1471-2148
卷号	15
摘要	Background: Long-established protein-coding genes may lose their coding potential during evolution (unitary gene loss). Members of the Poaceae family are a major food source and represent an ideal model clade for plant evolution research. However, the global pattern of unitary gene loss in Poaceae genomes as well as the evolutionary fate of lost genes are still less-investigated and remain largely elusive. Results: Using a locally developed pipeline, we identified 129 unitary gene loss events for long-established protein-coding genes from four representative species of Poaceae, i.e. brachypodium, rice, sorghum and maize. Functional annotation suggested that the lost genes in all or most of Poaceae species are enriched for genes involved in development and response to endogenous stimulus. We also found that 44 mutated genomic loci of lost genes, which we referred as relics, were still actively transcribed, and of which 84% (37 of 44) showed significantly differential expression across different tissues. More interestingly, we found that there were totally five expressed relics may function as competitive endogenous RNA in brachypodium, rice and sorghum genome. Conclusions: Based on comparative genomics and transcriptome data, we firstly compiled a comprehensive catalogue of unitary gene loss events in Poaceae species and characterized a statistically significant functional preference for these lost genes as well showed the potential of relics functioning as competitive endogenous RNAs in Poaceae genomes.
关键词	Unitary gene loss Poaceae Competitive endogenous RNA
学科领域	Evolutionary Biology ; Genetics & Heredity
DOI	10.1186/s12862-015-0345-x
收录类别	SCI
语种	英语
WOS关键词	REGULATORY GENES ; GENOME EVOLUTION ; PSEUDOGENES ; EXPRESSION ; DIVERGENCE ; SCENARIOS ; DELETION ; SORGHUM ; ROLES ; NOS
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000354078400001
出版者	BMC
文献子类	Article
出版地	LONDON
资助机构	China National 973 Program [2011CBA01103] ; 863 Programs [2006AA02Z334] ; State Key Laboratory of Protein and Plant Gene Research ; National Program for Support of Top-notch Young Professionals ; China Postdoctoral Science Foundation Grant [2014M560017] ; Chongqing Natural Science Foundation [cstc2012jjA80017]
作者邮箱	gaog@mail.cbi.pku.edu.cn
作品OA属性	Green Published, gold
引用统计	被引频次：11[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/26016
专题	系统与进化植物学国家重点实验室
作者单位	1.Peking Univ, Ctr Bioinformat, Coll Life Sci, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China 2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Zhao, Yi,Tang, Liang,Li, Zhe,et al. Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics[J]. BMC EVOLUTIONARY BIOLOGY,2015,15.
APA	Zhao, Yi,Tang, Liang,Li, Zhe,Jin, Jinpu,Luo, Jingchu,&Gao, Ge.(2015).Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics.BMC EVOLUTIONARY BIOLOGY,15.
MLA	Zhao, Yi,et al."Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics".BMC EVOLUTIONARY BIOLOGY 15(2015).

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