Draft genome of the living fossil Ginkgo biloba

doi:10.1186/s13742-016-0154-1

CORC > 植物研究所 > 中国科学院植物研究所 > 系统与进化植物学国家重点实验室

	Draft genome of the living fossil Ginkgo biloba
	Guan, Rui 3,4; Zhao, Yunpeng 2,5,6; Zhang, He 3,9; Fan, Guangyi 3; Liu, Xin ; Zhou, Wenbin 2,5,6; Shi, Chengcheng ; Wang, Jiahao ; Liu, Weiqing 10; Liang, Xinming
刊名	GIGASCIENCE
	2016
卷号	5
关键词	Ginkgo genome Evolution of LTR-RTs Tandem gene duplication Plant defense mechanism Gymnosperm evolution Whole genome duplication
ISSN号	2047-217X
DOI	10.1186/s13742-016-0154-1
文献子类	Article
英文摘要	Background: Ginkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution. Findings: The 10.61 Gb genome sequence containing 41,840 annotated genes was assembled in the present study. Repetitive sequences account for 76.58% of the assembled sequence, and long terminal repeat retrotransposons (LTR-RTs) are particularly prevalent. The diversity and abundance of LTR-RTs is due to their gradual accumulation and a remarkable amplification between 16 and 24 million years ago, and they contribute to the long introns and large genome. Whole genome duplication (WGD) may have occurred twice, with an ancient WGD consistent with that shown to occur in other seed plants, and a more recent event specific to ginkgo. Abundant gene clusters from tandem duplication were also evident, and enrichment of expanded gene families indicates a remarkable array of chemical and antibacterial defense pathways. Conclusions: The ginkgo genome consists mainly of LTR-RTs resulting from ancient gradual accumulation and two WGD events. The multiple defense mechanisms underlying the characteristic resilience of ginkgo are fostered by a remarkable enrichment in ancient duplicated and ginkgo-specific gene clusters. The present study sheds light on sequencing large genomes, and opens an avenue for further genetic and evolutionary research.
学科主题	Biology ; Multidisciplinary Sciences
出版地	OXFORD
WOS关键词	PICEA-GLAUCA GENOME ; FLOWERING PLANTS ; GENE ; EVOLUTION ; SEQUENCE ; CONIFERS ; ANCIENT ; FAMILY ; RETROTRANSPOSONS ; ANGIOSPERMS
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000388996700001
资助机构	Shenzhen Municipal Government [JSGG20130918102805062, JCYJ20120618172523025, JCYJ20150529150505656] ; Public Technology Research Project of Zhejiang Province [2014C32107] ; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31000102] ; CAS/SAFEA International Partnership Program for Creative Research TeamsChinese Academy of Sciences
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/24354]
专题	系统与进化植物学国家重点实验室
作者单位	1.Zhejiang Univ, Coll Life Sci, Key Lab Conservat Biol Endangered Wildlife, Minist Educ, Hangzhou 310058, Zhejiang, Peoples R China 2.BGI Shenzhen, Shenzhen 518083, Peoples R China 3.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 4.BGI Qingdao, Qingdao 266555, Peoples R China 5.Southeast Univ, Sch Biol Sci & Med Engn, State Key Lab Bioelect, Nanjing 210096, Jiangsu, Peoples R China 6.Zhejiang Univ, Inst Ecol, Lab Systemat & Evolutionary Bot & Biodivers, Hangzhou 310058, Zhejiang, Peoples R China 7.Zhejiang Univ, Conservat Ctr Gene Resources Endangered Wildlife, Hangzhou 310058, Zhejiang, Peoples R China 8.State Key Lab Qual Res Chinese Med, Macau, Peoples R China 9.Inst Chinese Med Sci, Macau, Peoples R China 10.Chinese Univ Hong Kong, Fac Med, Stanley Ho Ctr Emerging Infect Dis, Shatin, Hong Kong, Peoples R China
推荐引用方式 GB/T 7714	Guan, Rui,Zhao, Yunpeng,Zhang, He,et al. Draft genome of the living fossil Ginkgo biloba[J]. GIGASCIENCE,2016,5.
APA	Guan, Rui.,Zhao, Yunpeng.,Zhang, He.,Fan, Guangyi.,Liu, Xin.,...&Chen, Wenbin.(2016).Draft genome of the living fossil Ginkgo biloba.GIGASCIENCE,5.
MLA	Guan, Rui,et al."Draft genome of the living fossil Ginkgo biloba".GIGASCIENCE 5(2016).