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Gigascience. 2016 Nov 21;5(1):49.

Draft genome of the living fossil Ginkgo biloba.

Guan R1,2,3, Zhao Y4,5, Zhang H1,2,6, Fan G1,2,7, Liu X1, Zhou W4,5, Shi C1, Wang J1, Liu W8, Liang X1, Fu Y1,3, Ma K1, Zhao L4,5, Zhang F9, Lu Z3, Lee SM7, Xu X1, Wang J1,10, Yang H1,10, Fu C11,12, Ge S13, Chen W14,15.

Author information

1
BGI-Shenzhen, Shenzhen, 518083, China.
2
BGI-Qingdao, Qingdao, 266555, China.
3
State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
4
The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
5
Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Ecology and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, 310058, China.
6
Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong.
7
State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China.
8
BGI-Wuhan, BGI-Shenzhen, Wuhan, 430074, China.
9
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
10
James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China.
11
The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. cxfu@zju.edu.cn.
12
Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Ecology and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, 310058, China. cxfu@zju.edu.cn.
13
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. gesong@ibcas.ac.cn.
14
BGI-Shenzhen, Shenzhen, 518083, China. chenwenbin@genomics.cn.
15
BGI-Qingdao, Qingdao, 266555, China. chenwenbin@genomics.cn.

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.

KEYWORDS:

Evolution of LTR-RTs; Ginkgo genome; Gymnosperm evolution; Plant defense mechanism; Tandem gene duplication; Whole genome duplication

PMID:
27871309
PMCID:
PMC5118899
DOI:
10.1186/s13742-016-0154-1
[Indexed for MEDLINE]
Free PMC Article

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