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.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design Beijing Forestry University Beijing 100083 China

Beijing Ori Gene Science and Technology Co Ltd Beijing 102206 China

BioDiscovery Institute and Department of Biological Sciences University of North Texas Denton TX 76203 USA

Biology Department Brookhaven National Laboratory Upton NY 11973 USA

Centre of the Region Haná for Biotechnological and Agricultural Research Faculty of Science Palacký University 78301 Olomouc Czech Republic

College of Biological Sciences and Biotechnology Beijing Forestry University Beijing 100083 China

College of Biological Sciences China Agricultural University Beijing 100193 China

College of Horticulture and Plant Protection Yangzhou University Yangzhou 225009 China

College of Life Science Henan Normal University Xinxiang 453007 China

College of Life Sciences Peking University Beijing 100871 China

Department of Wood Anatomy and Utilization Research Institute of Wood Industry Chinese Academy of Forestry Beijing 100091 China

Institute of Botany Chinese Academy of Sciences Beijing 100093 China

Institute of Cellular and Molecular Botany University of Bonn Kirschallee 1 53115 Bonn Germany

School of Ecology and Nature conservation Beijing Forestry University Beijing 100083 China

State Key Laboratory of Protein and Plant Gene Research College of Life Sciences Peking University Beijing 100871 China

Wood Collections Chinese Academy of Forestry Beijing 100091 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

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