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

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The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements
Genome Biology ( IF 10.1 ) Pub Date : 2020-12-01 , DOI: 10.1186/s13059-020-02198-7
Ping-Li Liu _{1,

2} , Xi Zhang _{1,

2} , Jian-Feng Mao _{1,

2} , Yan-Ming Hong _{1,

2} , Ren-Gang Zhang ₃ , Yilan E _{1,

2} , Shuai Nie _{1,

2} , Kaihua Jia _{1,

2} , Chen-Kun Jiang ₄ , Jian He ₅ , Weiwei Shen _{1,

2} , Qizouhong He _{1,

2} , Wenqing Zheng _{1,

2} , Samar Abbas _{1,

2} , Pawan Kumar Jewaria _{1,

2} , Xuechan Tian _{1,

2} , Chang-Jun Liu ₆ , Xiaomei Jiang _{7,

8} , Yafang Yin _{7,

8} , Bo Liu _{7,

8} , Li Wang ₉ , Biao Jin ₉ , Yongpeng Ma ₁₀ , Zongbo Qiu ₁₁ , František Baluška ₁₂ , Jozef Šamaj ₁₃ , Xinqiang He ₁₄ , Shihui Niu _{1,

2} , Jianbo Xie _{1,

2} , Lei Xie ₅ , Huimin Xu ₁₅ , Hongzhi Kong ₁₆ , Song Ge ₁₆ , Richard A Dixon _{1,

17} , Yuannian Jiao ₁₆ , Jinxing Lin _{1,

2}

Affiliation

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.
College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China.
Beijing Ori-Gene Science and Technology Co., Ltd, Beijing, 102206, China.
College of Life Sciences, Peking University, Beijing, 100871, China.
School of Ecology and Nature conservation, Beijing Forestry University, Beijing, 100083, China.
Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA.
Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China.
Department of Wood Anatomy and Utilization, Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.
College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China.
Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
College of Life Science, Henan Normal University, Xinxiang, 453007, China.
Institute of Cellular and Molecular Botany (IZMB), University of Bonn, Kirschallee 1, 53115, Bonn, Germany.
Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, 78301, Olomouc, Czech Republic.
State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA.

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 γ 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.

更新日期：2020-12-01

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