The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements

doi:10.1186/s13059-020-02198-7

	The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements
	Liu, Ping-Li ; Zhang, Xi ; Mao, Jian-Feng ; Hong, Yan-Ming ; Zhang, Ren-Gang ; Yilan, E.; Nie, Shuai 1; Jia, Kaihua 1; Jiang, Chen-Kun ; He, Jian 4; Shen, Weiwei 1; He, Qizouhong 1; Zheng, Wenqing 1; Abbas, Samar 1; Jewaria, Pawan Kumar 1; Tian, Xuechan 1; Liu, Chang-jun ; Jiang, Xiaomei 6,7; Yin, Yafang 6,7; Liu, Bo 6,7; Wang, Li 8; Jin, Biao 8; Ma, Yongpeng 9; Qiu, Zongbo 10; Baluska, Frantisek 11; Samaj, Jozef 12; He, Xinqiang 13; Niu, Shihui 1; Xie, Jianbo 1; Xie, Lei 4; Xu, Huimin 14; Kong, Hongzhi15 ; Ge, Song15 ; Dixon, Richard A.; Jiao, Yuannian15 ; Lin, Jinxing 1
	2020
发表期刊	GENOME BIOLOGY
ISSN	1474-760X
卷号	21 期号:1
摘要	Background Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species. Results Here, we report a chromosome-scale assembly of the T. sinense genome. We assemble the 1.07 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes. Phylogenomic analyses verify that the Trochodendrales and core eudicots are sister lineages and showed that two whole-genome duplications occurred in the Trochodendrales approximately 82 and 59 million years ago. Synteny analyses suggest that the gamma event, resulting in paleohexaploidy, may have only happened in core eudicots. Interestingly, we find that vessel elements are present in T. sinense, which has two orthologs of AtVND7, the master regulator of vessel formation. T. sinense also has several key genes regulated by or regulating TsVND7.2 and their regulatory relationship resembles that in Arabidopsis thaliana. Resequencing and population genomics reveals high levels of genetic diversity of T. sinense and identifies four refugia in China. Conclusions The T. sinense genome provides a unique reference for inferring the early evolution of eudicots and the mechanisms underlying vessel element formation. Population genomics analysis of T. sinense reveals its genetic diversity and geographic structure with implications for conservation.
关键词	Tetracentron sinense Vessel Phylogenomic Whole genome duplication VND7 Resequencing Genetic diversity
学科领域	Biotechnology & Applied Microbiology ; Genetics & Heredity
DOI	10.1186/s13059-020-02198-7
收录类别	SCI
语种	英语
WOS关键词	MULTIPLE SEQUENCE ALIGNMENT ; TRANSCRIPTION FACTORS ; WALL BIOSYNTHESIS ; WASHINGTON-STATE ; GENE-EXPRESSION ; DIRECT TARGET ; TROCHODENDRACEAE ; PROTEIN ; PHYLOGENY ; XYLEM
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:000595383800001
出版者	BMC
文献子类	Article
出版地	LONDON
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31530084] ; Fundamental Research Funds for the Central UniversitiesFundamental Research Funds for the Central Universities [2019ZY28] ; Program of Introducing Talents of Discipline to UniversitiesMinistry of Education, China - 111 Project [B13007] ; National Science Foundation for Young Scientists of China [32000558]
作者邮箱	jiaoyn@ibcas.ac.cn ; linjx@ibcas.ac.cn
作品OA属性	Green Published, gold
引用统计	被引频次：21[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/2S10CLM1/21504
专题	系统与进化植物学国家重点实验室
作者单位	1.Beijing Forestry Univ, Beijing Adv Innovat Ctr Tree Breeding Mol Design, Beijing 100083, Peoples R China 2.Beijing Forestry Univ, Coll Biol Sci & Biotechnol, Beijing 100083, Peoples R China 3.Beijing Ori Gene Sci & Technol Co Ltd, Beijing 102206, Peoples R China 4.Peking Univ, Coll Life Sci, Beijing 100871, Peoples R China 5.Beijing Forestry Univ, Sch Ecol & Nat Conservat, Beijing 100083, Peoples R China 6.Brookhaven Natl Lab, Biol Dept, Upton, NY 11973 USA 7.Chinese Acad Forestry, Wood Collect WOODPEDIA, Beijing 100091, Peoples R China 8.Chinese Acad Forestry, Res Inst Wood Ind, Dept Wood Anat & Utilizat, Beijing 100091, Peoples R China 9.Yangzhou Univ, Coll Hort & Plant Protect, Yangzhou 225009, Jiangsu, Peoples R China 10.Chinese Acad Sci, Kunming Inst Bot, Yunnan Key Lab Integrat Conservat Plant Species, Kunming 650201, Yunnan, Peoples R China 11.Henan Normal Univ, Coll Life Sci, Xinxiang 453007, Henan, Peoples R China 12.Univ Bonn, Inst Cellular & Mol Bot IZMB, Kirschallee 1, D-53115 Bonn, Germany 13.Palacky Univ, Fac Sci, Ct Reg Hana Biotechnol & Agr Res, Olomouc 78301, Czech Republic 14.Peking Univ, Coll Life Sci, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China 15.China Agr Univ, Coll Biol Sci, Beijing 100193, Peoples R China 16.Chinese Acad Sci, Inst Bot, Beijing 100093, Peoples R China 17.Dixon, Richard A.] Univ North Texas, BioDiscovery Inst, Denton, TX 76203 USA 18.Dixon, Richard A.] Univ North Texas, Dept Biol Sci, Denton, TX 76203 USA
推荐引用方式 GB/T 7714	Liu, Ping-Li,Zhang, Xi,Mao, Jian-Feng,et al. The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements[J]. GENOME BIOLOGY,2020,21(1).
APA	Liu, Ping-Li.,Zhang, Xi.,Mao, Jian-Feng.,Hong, Yan-Ming.,Zhang, Ren-Gang.,...&Lin, Jinxing.(2020).The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements.GENOME BIOLOGY,21(1).
MLA	Liu, Ping-Li,et al."The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements".GENOME BIOLOGY 21.1(2020).

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