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Draft genome of the living fossil Ginkgo biloba
Guan R.1,4,5; Zhao Y.2,6; Zhang H.1,4,8; Fan G.1,4,7; Liu X.1; Zhou W.2,6; Shi C.1; Wang J.1; Liu W.9; Liang X.1; Fu Y.1,5; Ma K.1; Zhao L.2,6; Zhang F.3; Lu Z.5; Lee S.M.-Y.7; Xu X.1; Wang J.1,10; Yang H.1,10; Fu C.2,6; Ge S.3; Chen W.1,4
2016-11-21
Source PublicationGigaScience
ISSN2047217X
Volume5Issue:1
Abstract

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.

KeywordEvolution Of Ltr-rts Ginkgo Genome Gymnosperm Evolution Plant Defense Mechanism Tandem Gene Duplication Whole Genome Duplication
DOI10.1186/s13742-016-0154-1
URLView the original
Language英语
WOS Research AreaLife Sciences & Biomedicine - Other Topics ; Science & Technology - Other Topics
WOS SubjectBiology ; Multidisciplinary Sciences
WOS IDwos:000388996700001
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Cited Times [WOS]:75   [WOS Record]     [Related Records in WOS]
Document TypeJournal article
CollectionInstitute of Chinese Medical Sciences
Affiliation1.BGI-Shenzhen, Shenzhen 518083, China
2.The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
3.State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
4.BGI-Qingdao, Qingdao 266555, China
5.State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
6.Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Ecology and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou 310058, China
7.State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China
8.Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
9.BGI-Wuhan, BGI-Shenzhen, Wuhan 430074, China
10.James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
Recommended Citation
GB/T 7714
Guan R.,Zhao Y.,Zhang H.,et al. Draft genome of the living fossil Ginkgo biloba[J]. GigaScience,2016,5(1).
APA Guan R..,Zhao Y..,Zhang H..,Fan G..,Liu X..,...&Chen W..(2016).Draft genome of the living fossil Ginkgo biloba.GigaScience,5(1).
MLA Guan R.,et al."Draft genome of the living fossil Ginkgo biloba".GigaScience 5.1(2016).
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