The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements
Abstract 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 e...
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| Format: | Article |
| Language: | English |
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BMC
2020-12-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-020-02198-7 |
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doaj-981d4c869e0e4e15a60ac64e7a863fbd |
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Article |
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DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Ping-Li Liu Xi Zhang Jian-Feng Mao Yan-Ming Hong Ren-Gang Zhang Yilan E Shuai Nie Kaihua Jia Chen-Kun Jiang Jian He Weiwei Shen Qizouhong He Wenqing Zheng Samar Abbas Pawan Kumar Jewaria Xuechan Tian Chang-jun Liu Xiaomei Jiang Yafang Yin Bo Liu Li Wang Biao Jin Yongpeng Ma Zongbo Qiu František Baluška Jozef Šamaj Xinqiang He Shihui Niu Jianbo Xie Lei Xie Huimin Xu Hongzhi Kong Song Ge Richard A. Dixon Yuannian Jiao Jinxing Lin |
| spellingShingle |
Ping-Li Liu Xi Zhang Jian-Feng Mao Yan-Ming Hong Ren-Gang Zhang Yilan E Shuai Nie Kaihua Jia Chen-Kun Jiang Jian He Weiwei Shen Qizouhong He Wenqing Zheng Samar Abbas Pawan Kumar Jewaria Xuechan Tian Chang-jun Liu Xiaomei Jiang Yafang Yin Bo Liu Li Wang Biao Jin Yongpeng Ma Zongbo Qiu František Baluška Jozef Šamaj Xinqiang He Shihui Niu Jianbo Xie Lei Xie Huimin Xu Hongzhi Kong Song Ge Richard A. Dixon Yuannian Jiao Jinxing Lin The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements Genome Biology Tetracentron sinense Vessel Phylogenomic Whole genome duplication VND7 Resequencing |
| author_facet |
Ping-Li Liu Xi Zhang Jian-Feng Mao Yan-Ming Hong Ren-Gang Zhang Yilan E Shuai Nie Kaihua Jia Chen-Kun Jiang Jian He Weiwei Shen Qizouhong He Wenqing Zheng Samar Abbas Pawan Kumar Jewaria Xuechan Tian Chang-jun Liu Xiaomei Jiang Yafang Yin Bo Liu Li Wang Biao Jin Yongpeng Ma Zongbo Qiu František Baluška Jozef Šamaj Xinqiang He Shihui Niu Jianbo Xie Lei Xie Huimin Xu Hongzhi Kong Song Ge Richard A. Dixon Yuannian Jiao Jinxing Lin |
| author_sort |
Ping-Li Liu |
| title |
The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements |
| title_short |
The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements |
| title_full |
The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements |
| title_fullStr |
The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements |
| title_full_unstemmed |
The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements |
| title_sort |
tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements |
| publisher |
BMC |
| series |
Genome Biology |
| issn |
1474-760X |
| publishDate |
2020-12-01 |
| description |
Abstract 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. |
| topic |
Tetracentron sinense Vessel Phylogenomic Whole genome duplication VND7 Resequencing |
| url |
https://doi.org/10.1186/s13059-020-02198-7 |
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doaj-981d4c869e0e4e15a60ac64e7a863fbd2020-12-06T12:53:20ZengBMCGenome Biology1474-760X2020-12-0121113010.1186/s13059-020-02198-7The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elementsPing-Li Liu0Xi Zhang1Jian-Feng Mao2Yan-Ming Hong3Ren-Gang Zhang4Yilan E5Shuai Nie6Kaihua Jia7Chen-Kun Jiang8Jian He9Weiwei Shen10Qizouhong He11Wenqing Zheng12Samar Abbas13Pawan Kumar Jewaria14Xuechan Tian15Chang-jun Liu16Xiaomei Jiang17Yafang Yin18Bo Liu19Li Wang20Biao Jin21Yongpeng Ma22Zongbo Qiu23František Baluška24Jozef Šamaj25Xinqiang He26Shihui Niu27Jianbo Xie28Lei Xie29Huimin Xu30Hongzhi Kong31Song Ge32Richard A. Dixon33Yuannian Jiao34Jinxing Lin35Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityBeijing Ori-Gene Science and Technology Co., LtdBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityCollege of Life Sciences, Peking UniversitySchool of Ecology and Nature conservation, Beijing Forestry UniversityBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityBiology Department, Brookhaven National LaboratoryWood Collections (WOODPEDIA), Chinese Academy of ForestryWood Collections (WOODPEDIA), Chinese Academy of ForestryWood Collections (WOODPEDIA), Chinese Academy of ForestryCollege of Horticulture and Plant Protection, Yangzhou UniversityCollege of Horticulture and Plant Protection, Yangzhou UniversityYunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of SciencesCollege of Life Science, Henan Normal UniversityInstitute of Cellular and Molecular Botany (IZMB), University of BonnCentre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký UniversityState Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking UniversityBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversitySchool of Ecology and Nature conservation, Beijing Forestry UniversityCollege of Biological Sciences, China Agricultural UniversityInstitute of Botany, Chinese Academy of SciencesInstitute of Botany, Chinese Academy of SciencesBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityInstitute of Botany, Chinese Academy of SciencesBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry UniversityAbstract 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.https://doi.org/10.1186/s13059-020-02198-7Tetracentron sinenseVesselPhylogenomicWhole genome duplicationVND7Resequencing |