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...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Ping-Li Liu [verfasserIn] Xi Zhang [verfasserIn] Jian-Feng Mao [verfasserIn] Yan-Ming Hong [verfasserIn] Ren-Gang Zhang [verfasserIn] Yilan E [verfasserIn] Shuai Nie [verfasserIn] Kaihua Jia [verfasserIn] Chen-Kun Jiang [verfasserIn] Jian He [verfasserIn] Weiwei Shen [verfasserIn] Qizouhong He [verfasserIn] Wenqing Zheng [verfasserIn] Samar Abbas [verfasserIn] Pawan Kumar Jewaria [verfasserIn] Xuechan Tian [verfasserIn] Chang-jun Liu [verfasserIn] Xiaomei Jiang [verfasserIn] Yafang Yin [verfasserIn] Bo Liu [verfasserIn] Li Wang [verfasserIn] Biao Jin [verfasserIn] Yongpeng Ma [verfasserIn] Zongbo Qiu [verfasserIn] František Baluška [verfasserIn] Jozef Šamaj [verfasserIn] Xinqiang He [verfasserIn] Shihui Niu [verfasserIn] Jianbo Xie [verfasserIn] Lei Xie [verfasserIn] Huimin Xu [verfasserIn] Hongzhi Kong [verfasserIn] Song Ge [verfasserIn] Richard A. Dixon [verfasserIn] Yuannian Jiao [verfasserIn] Jinxing Lin [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2020 |
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| Übergeordnetes Werk: |
In: Genome Biology - BMC, 2014, 21(2020), 1, Seite 30 |
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| Übergeordnetes Werk: |
volume:21 ; year:2020 ; number:1 ; pages:30 |
| Links: |
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| DOI / URN: |
10.1186/s13059-020-02198-7 |
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DOAJ072322012 |
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| 520 | |a 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. | ||
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10.1186/s13059-020-02198-7 doi (DE-627)DOAJ072322012 (DE-599)DOAJ981d4c869e0e4e15a60ac64e7a863fbd DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Ping-Li Liu verfasserin aut The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Tetracentron sinense Vessel Phylogenomic Whole genome duplication VND7 Resequencing Biology (General) Genetics Xi Zhang verfasserin aut Jian-Feng Mao verfasserin aut Yan-Ming Hong verfasserin aut Ren-Gang Zhang verfasserin aut Yilan E verfasserin aut Shuai Nie verfasserin aut Kaihua Jia verfasserin aut Chen-Kun Jiang verfasserin aut Jian He verfasserin aut Weiwei Shen verfasserin aut Qizouhong He verfasserin aut Wenqing Zheng verfasserin aut Samar Abbas verfasserin aut Pawan Kumar Jewaria verfasserin aut Xuechan Tian verfasserin aut Chang-jun Liu verfasserin aut Xiaomei Jiang verfasserin aut Yafang Yin verfasserin aut Bo Liu verfasserin aut Li Wang verfasserin aut Biao Jin verfasserin aut Yongpeng Ma verfasserin aut Zongbo Qiu verfasserin aut František Baluška verfasserin aut Jozef Šamaj verfasserin aut Xinqiang He verfasserin aut Shihui Niu verfasserin aut Jianbo Xie verfasserin aut Lei Xie verfasserin aut Huimin Xu verfasserin aut Hongzhi Kong verfasserin aut Song Ge verfasserin aut Richard A. Dixon verfasserin aut Yuannian Jiao verfasserin aut Jinxing Lin verfasserin aut In Genome Biology BMC, 2014 21(2020), 1, Seite 30 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:21 year:2020 number:1 pages:30 https://doi.org/10.1186/s13059-020-02198-7 kostenfrei https://doaj.org/article/981d4c869e0e4e15a60ac64e7a863fbd kostenfrei https://doi.org/10.1186/s13059-020-02198-7 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 21 2020 1 30 |
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10.1186/s13059-020-02198-7 doi (DE-627)DOAJ072322012 (DE-599)DOAJ981d4c869e0e4e15a60ac64e7a863fbd DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Ping-Li Liu verfasserin aut The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Tetracentron sinense Vessel Phylogenomic Whole genome duplication VND7 Resequencing Biology (General) Genetics Xi Zhang verfasserin aut Jian-Feng Mao verfasserin aut Yan-Ming Hong verfasserin aut Ren-Gang Zhang verfasserin aut Yilan E verfasserin aut Shuai Nie verfasserin aut Kaihua Jia verfasserin aut Chen-Kun Jiang verfasserin aut Jian He verfasserin aut Weiwei Shen verfasserin aut Qizouhong He verfasserin aut Wenqing Zheng verfasserin aut Samar Abbas verfasserin aut Pawan Kumar Jewaria verfasserin aut Xuechan Tian verfasserin aut Chang-jun Liu verfasserin aut Xiaomei Jiang verfasserin aut Yafang Yin verfasserin aut Bo Liu verfasserin aut Li Wang verfasserin aut Biao Jin verfasserin aut Yongpeng Ma verfasserin aut Zongbo Qiu verfasserin aut František Baluška verfasserin aut Jozef Šamaj verfasserin aut Xinqiang He verfasserin aut Shihui Niu verfasserin aut Jianbo Xie verfasserin aut Lei Xie verfasserin aut Huimin Xu verfasserin aut Hongzhi Kong verfasserin aut Song Ge verfasserin aut Richard A. Dixon verfasserin aut Yuannian Jiao verfasserin aut Jinxing Lin verfasserin aut In Genome Biology BMC, 2014 21(2020), 1, Seite 30 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:21 year:2020 number:1 pages:30 https://doi.org/10.1186/s13059-020-02198-7 kostenfrei https://doaj.org/article/981d4c869e0e4e15a60ac64e7a863fbd kostenfrei https://doi.org/10.1186/s13059-020-02198-7 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 21 2020 1 30 |
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10.1186/s13059-020-02198-7 doi (DE-627)DOAJ072322012 (DE-599)DOAJ981d4c869e0e4e15a60ac64e7a863fbd DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Ping-Li Liu verfasserin aut The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Tetracentron sinense Vessel Phylogenomic Whole genome duplication VND7 Resequencing Biology (General) Genetics Xi Zhang verfasserin aut Jian-Feng Mao verfasserin aut Yan-Ming Hong verfasserin aut Ren-Gang Zhang verfasserin aut Yilan E verfasserin aut Shuai Nie verfasserin aut Kaihua Jia verfasserin aut Chen-Kun Jiang verfasserin aut Jian He verfasserin aut Weiwei Shen verfasserin aut Qizouhong He verfasserin aut Wenqing Zheng verfasserin aut Samar Abbas verfasserin aut Pawan Kumar Jewaria verfasserin aut Xuechan Tian verfasserin aut Chang-jun Liu verfasserin aut Xiaomei Jiang verfasserin aut Yafang Yin verfasserin aut Bo Liu verfasserin aut Li Wang verfasserin aut Biao Jin verfasserin aut Yongpeng Ma verfasserin aut Zongbo Qiu verfasserin aut František Baluška verfasserin aut Jozef Šamaj verfasserin aut Xinqiang He verfasserin aut Shihui Niu verfasserin aut Jianbo Xie verfasserin aut Lei Xie verfasserin aut Huimin Xu verfasserin aut Hongzhi Kong verfasserin aut Song Ge verfasserin aut Richard A. Dixon verfasserin aut Yuannian Jiao verfasserin aut Jinxing Lin verfasserin aut In Genome Biology BMC, 2014 21(2020), 1, Seite 30 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:21 year:2020 number:1 pages:30 https://doi.org/10.1186/s13059-020-02198-7 kostenfrei https://doaj.org/article/981d4c869e0e4e15a60ac64e7a863fbd kostenfrei https://doi.org/10.1186/s13059-020-02198-7 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 21 2020 1 30 |
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10.1186/s13059-020-02198-7 doi (DE-627)DOAJ072322012 (DE-599)DOAJ981d4c869e0e4e15a60ac64e7a863fbd DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Ping-Li Liu verfasserin aut The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Tetracentron sinense Vessel Phylogenomic Whole genome duplication VND7 Resequencing Biology (General) Genetics Xi Zhang verfasserin aut Jian-Feng Mao verfasserin aut Yan-Ming Hong verfasserin aut Ren-Gang Zhang verfasserin aut Yilan E verfasserin aut Shuai Nie verfasserin aut Kaihua Jia verfasserin aut Chen-Kun Jiang verfasserin aut Jian He verfasserin aut Weiwei Shen verfasserin aut Qizouhong He verfasserin aut Wenqing Zheng verfasserin aut Samar Abbas verfasserin aut Pawan Kumar Jewaria verfasserin aut Xuechan Tian verfasserin aut Chang-jun Liu verfasserin aut Xiaomei Jiang verfasserin aut Yafang Yin verfasserin aut Bo Liu verfasserin aut Li Wang verfasserin aut Biao Jin verfasserin aut Yongpeng Ma verfasserin aut Zongbo Qiu verfasserin aut František Baluška verfasserin aut Jozef Šamaj verfasserin aut Xinqiang He verfasserin aut Shihui Niu verfasserin aut Jianbo Xie verfasserin aut Lei Xie verfasserin aut Huimin Xu verfasserin aut Hongzhi Kong verfasserin aut Song Ge verfasserin aut Richard A. Dixon verfasserin aut Yuannian Jiao verfasserin aut Jinxing Lin verfasserin aut In Genome Biology BMC, 2014 21(2020), 1, Seite 30 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:21 year:2020 number:1 pages:30 https://doi.org/10.1186/s13059-020-02198-7 kostenfrei https://doaj.org/article/981d4c869e0e4e15a60ac64e7a863fbd kostenfrei https://doi.org/10.1186/s13059-020-02198-7 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 21 2020 1 30 |
| allfieldsSound |
10.1186/s13059-020-02198-7 doi (DE-627)DOAJ072322012 (DE-599)DOAJ981d4c869e0e4e15a60ac64e7a863fbd DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Ping-Li Liu verfasserin aut The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Tetracentron sinense Vessel Phylogenomic Whole genome duplication VND7 Resequencing Biology (General) Genetics Xi Zhang verfasserin aut Jian-Feng Mao verfasserin aut Yan-Ming Hong verfasserin aut Ren-Gang Zhang verfasserin aut Yilan E verfasserin aut Shuai Nie verfasserin aut Kaihua Jia verfasserin aut Chen-Kun Jiang verfasserin aut Jian He verfasserin aut Weiwei Shen verfasserin aut Qizouhong He verfasserin aut Wenqing Zheng verfasserin aut Samar Abbas verfasserin aut Pawan Kumar Jewaria verfasserin aut Xuechan Tian verfasserin aut Chang-jun Liu verfasserin aut Xiaomei Jiang verfasserin aut Yafang Yin verfasserin aut Bo Liu verfasserin aut Li Wang verfasserin aut Biao Jin verfasserin aut Yongpeng Ma verfasserin aut Zongbo Qiu verfasserin aut František Baluška verfasserin aut Jozef Šamaj verfasserin aut Xinqiang He verfasserin aut Shihui Niu verfasserin aut Jianbo Xie verfasserin aut Lei Xie verfasserin aut Huimin Xu verfasserin aut Hongzhi Kong verfasserin aut Song Ge verfasserin aut Richard A. Dixon verfasserin aut Yuannian Jiao verfasserin aut Jinxing Lin verfasserin aut In Genome Biology BMC, 2014 21(2020), 1, Seite 30 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:21 year:2020 number:1 pages:30 https://doi.org/10.1186/s13059-020-02198-7 kostenfrei https://doaj.org/article/981d4c869e0e4e15a60ac64e7a863fbd kostenfrei https://doi.org/10.1186/s13059-020-02198-7 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 21 2020 1 30 |
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Ping-Li Liu @@aut@@ Xi Zhang @@aut@@ Jian-Feng Mao @@aut@@ Yan-Ming Hong @@aut@@ Ren-Gang Zhang @@aut@@ Yilan E @@aut@@ Shuai Nie @@aut@@ Kaihua Jia @@aut@@ Chen-Kun Jiang @@aut@@ Jian He @@aut@@ Weiwei Shen @@aut@@ Qizouhong He @@aut@@ Wenqing Zheng @@aut@@ Samar Abbas @@aut@@ Pawan Kumar Jewaria @@aut@@ Xuechan Tian @@aut@@ Chang-jun Liu @@aut@@ Xiaomei Jiang @@aut@@ Yafang Yin @@aut@@ Bo Liu @@aut@@ Li Wang @@aut@@ Biao Jin @@aut@@ Yongpeng Ma @@aut@@ Zongbo Qiu @@aut@@ František Baluška @@aut@@ Jozef Šamaj @@aut@@ Xinqiang He @@aut@@ Shihui Niu @@aut@@ Jianbo Xie @@aut@@ Lei Xie @@aut@@ Huimin Xu @@aut@@ Hongzhi Kong @@aut@@ Song Ge @@aut@@ Richard A. Dixon @@aut@@ Yuannian Jiao @@aut@@ Jinxing Lin @@aut@@ |
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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. 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tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements |
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The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements |
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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. |
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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. |
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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. |
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