Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of Two Oryza Species

doi:10.1093/molbev/msv196

	Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of Two Oryza Species
	Guo, Jie ; Liu, Rong ; Huang, Lei ; Zheng, Xiao-Ming ; Liu, Ping-Li ; Du, Yu-Su ; Cai, Zhe ; Zhou, Lian ; Wei, Xing-Hua ; Zhang, Fu-Min ; Ge, Song8,9
	2016
发表期刊	MOLECULAR BIOLOGY AND EVOLUTION
ISSN	0737-4038
卷号	33 期号:1 页码:62-78
摘要	Ecological speciation is a common mechanism by which new species arise. Despite great efforts, the role of gene expression in ecological divergence and speciation is poorly understood. Here, we conducted a genome-wide gene expression investigation of two Oryza species that are evolutionarily young and distinct in ecology and morphology. Using digital gene expression technology and the paired-end RNA sequencing method, we obtained 21,415 expressed genes across three reproduction-related tissues. Of them, approximately 8% (1,717) differed significantly in expression levels between the two species and these differentially expressed genes are randomly distributed across the genome. Moreover, 62% (1,064) of the differentially expressed genes exhibited a signature of directional selection in at least one species. Importantly, the genes with differential expression between species evolved more rapidly at the 50 flanking sequences than the genes without differential expression relative to coding sequences, suggesting that cis-regulatory changes are likely adaptive and play an important role in the ecological divergence of the two species. Finally, we showed evidence of significant differentiation between species in phenotype traits and observed that genes with differential expression were overrepresented with functional terms involving phenotypic and ecological differentiation between the two species, including reproduction-and stress-related characteristics. Our findings demonstrate that ecological speciation is associated with widespread and adaptive alterations in genome-wide gene expression and provide new insights into the importance of regulatory evolution in ecological speciation in plants.
关键词	ecological speciation expression evolution adaptation wild rice
学科领域	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
DOI	10.1093/molbev/msv196
收录类别	SCI
语种	英语
WOS关键词	WILD-RICE ; NATURAL-SELECTION ; SEVERE BOTTLENECK ; EVO-DEVO ; RNA-SEQ ; EVOLUTION ; SPECIATION ; PATTERNS ; DIFFERENTIATION ; TRANSCRIPTOMICS
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000369992600005
出版者	OXFORD UNIV PRESS
文献子类	Article
出版地	OXFORD
EISSN	1537-1719
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [91231201, 30990240, 31301035]
作者邮箱	gesong@ibcas.ac.cn
作品OA属性	Bronze
引用统计	被引频次：23[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/2S10CLM1/25076
专题	系统与进化植物学国家重点实验室
作者单位	1.[Guo, Jie 2.Liu, Rong 3.Huang, Lei 4.Zheng, Xiao-Ming 5.Liu, Ping-Li 6.Du, Yu-Su 7.Cai, Zhe 8.Zhou, Lian 9.Zhang, Fu-Min 10.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 11.[Liu, Rong 12.Univ Chinese Acad Sci, Beijing, Peoples R China 13.China Natl Rice Res Inst, State Key Lab Rice Biol, Hangzhou, Zhejiang, Peoples R China
推荐引用方式 GB/T 7714	Guo, Jie,Liu, Rong,Huang, Lei,et al. Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of Two Oryza Species[J]. MOLECULAR BIOLOGY AND EVOLUTION,2016,33(1):62-78.
APA	Guo, Jie.,Liu, Rong.,Huang, Lei.,Zheng, Xiao-Ming.,Liu, Ping-Li.,...&Ge, Song.(2016).Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of Two Oryza Species.MOLECULAR BIOLOGY AND EVOLUTION,33(1),62-78.
MLA	Guo, Jie,et al."Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of Two Oryza Species".MOLECULAR BIOLOGY AND EVOLUTION 33.1(2016):62-78.

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