Genome-Wide Analysis Indicates Lineage-Specific Gene Loss during Papilionoideae Evolution

doi:10.1093/gbe/evw021

	Genome-Wide Analysis Indicates Lineage-Specific Gene Loss during Papilionoideae Evolution
	Gu, Yongzhe 1; Xing, Shilai 1; He, Chaoying
	2016
发表期刊	GENOME BIOLOGY AND EVOLUTION
ISSN	1759-6653
卷号	8 期号:3 页码:635-648
摘要	Gene loss is the driving force for changes in genome and morphology; however, this particular evolutionary event has been poorly investigated in leguminous plants. Legumes (Fabaceae) have some lineage-specific and diagnostic characteristics that are distinct from other angiosperms. To understand the potential role of gene loss in the evolution of legumes, we compared six genome-sequenced legume species of Papilionoideae, the largest representative clade of Fabaceae, such as Glycine max, with 34 nonlegume plant species, such as Arabidopsis thaliana. The results showed that the putative orthologs of the 34 Arabidopsis genes belonging to 29 gene families were absent in these legume species but these were conserved in the sequenced nonlegume angiosperm lineages. Further evolutionary analyses indicated that the orthologs of these genes were almost completely lost in the Papillionoideae ancestors, thus designated as the legume lost genes (LLGs), and these underwent purifying selection in nonlegume plants. Most LLGs were functionally unknown. In Arabidopsis, two LLGs were well-known genes that played a role in plant immunity such as HARMLESS TO OZONE LAYER 1 and HOPZ-ACTIVATED RESISTANCE 1, and 16 additional LLGs were predicted to participate in plant-pathogen interactions in in silico expression and protein-protein interaction network analyses. Most of these LLGs' orthologs in various plants were also found to be associated with biotic stress response, indicating the conserved role of these genes in plant defense. The evolutionary implication of LLGs during the development of the ability of symbiotic nitrogen fixation involving plant and bacterial interactions, which is a well-known characteristic of most legumes, is also discussed. Our work sheds light on the evolutionary implication of gene loss events in Papilionoideae evolution, as well as provides new insights into crop design to improve nitrogen fixation capacity.
关键词	defense response gene loss genome evolution legume nitrogen fixation
学科领域	Evolutionary Biology ; Genetics & Heredity
DOI	10.1093/gbe/evw021
收录类别	SCI
语种	英语
WOS关键词	HOMOLOGOUS RECOMBINATION ; PROVIDES INSIGHT ; ORPHAN GENES ; DNA-REPAIR ; ARABIDOPSIS ; PROTEIN ; LEGUME ; PLANT ; EXPRESSION ; SEQUENCE
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000373839200015
出版者	OXFORD UNIV PRESS
文献子类	Article
出版地	OXFORD
资助机构	Chinese Academy of SciencesChinese Academy of Sciences [XDA08010105] ; CAS/SAFEA International Partner Program for Creative Research Teams of Systematic and Evolutionary Botany
作者邮箱	chaoying@ibcas.ac.cn
作品OA属性	gold, Green Published, Green Submitted
引用统计	被引频次：9[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/2S10CLM1/25013
专题	系统与进化植物学国家重点实验室
作者单位	1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Nanxincun 20, Beijing 100093, Peoples R China 2.Grad Univ, Chinese Acad Sci, Yuquan Rd 19, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Gu, Yongzhe,Xing, Shilai,He, Chaoying. Genome-Wide Analysis Indicates Lineage-Specific Gene Loss during Papilionoideae Evolution[J]. GENOME BIOLOGY AND EVOLUTION,2016,8(3):635-648.
APA	Gu, Yongzhe,Xing, Shilai,&He, Chaoying.(2016).Genome-Wide Analysis Indicates Lineage-Specific Gene Loss during Papilionoideae Evolution.GENOME BIOLOGY AND EVOLUTION,8(3),635-648.
MLA	Gu, Yongzhe,et al."Genome-Wide Analysis Indicates Lineage-Specific Gene Loss during Papilionoideae Evolution".GENOME BIOLOGY AND EVOLUTION 8.3(2016):635-648.

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