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The complex jujube genome provides insights into fruit tree biology

Identifieur interne : 000885 ( Main/Exploration ); précédent : 000884; suivant : 000886

The complex jujube genome provides insights into fruit tree biology

Auteurs : Meng-Jun Liu [République populaire de Chine] ; Jin Zhao [République populaire de Chine] ; Qing-Le Cai [République populaire de Chine] ; Guo-Cheng Liu [République populaire de Chine] ; Jiu-Rui Wang [République populaire de Chine] ; Zhi-Hui Zhao [République populaire de Chine] ; Ping Liu [République populaire de Chine] ; Li Dai [République populaire de Chine] ; Guijun Yan [Australie] ; Wen-Jiang Wang [République populaire de Chine] ; Xian-Song Li [République populaire de Chine] ; Yan Chen [République populaire de Chine] ; Yu-Dong Sun [République populaire de Chine] ; Zhi-Guo Liu [République populaire de Chine] ; Min-Juan Lin [République populaire de Chine] ; Jing Xiao [République populaire de Chine] ; Ying-Ying Chen [République populaire de Chine] ; Xiao-Feng Li [République populaire de Chine] ; Bin Wu [République populaire de Chine] ; Yong Ma [République populaire de Chine] ; Jian-Bo Jian [République populaire de Chine] ; Wei Yang [République populaire de Chine] ; Zan Yuan [République populaire de Chine] ; Xue-Chao Sun [République populaire de Chine] ; Yan-Li Wei [République populaire de Chine] ; Li-Li Yu [République populaire de Chine] ; Chi Zhang [République populaire de Chine] ; Sheng-Guang Liao [République populaire de Chine] ; Rong-Jun He [République populaire de Chine] ; Xuan-Min Guang [République populaire de Chine] ; Zhuo Wang [République populaire de Chine] ; Yue-Yang Zhang [République populaire de Chine] ; Long-Hai Luo [République populaire de Chine]

Source :

RBID : PMC:4220462

Abstract

The jujube (Ziziphus jujuba Mill.), a member of family Rhamnaceae, is a major dry fruit and a traditional herbal medicine for more than one billion people. Here we present a high-quality sequence for the complex jujube genome, the first genome sequence of Rhamnaceae, using an integrated strategy. The final assembly spans 437.65 Mb (98.6% of the estimated) with 321.45 Mb anchored to the 12 pseudo-chromosomes and contains 32,808 genes. The jujube genome has undergone frequent inter-chromosome fusions and segmental duplications, but no recent whole-genome duplication. Further analyses of the jujube-specific genes and transcriptome data from 15 tissues reveal the molecular mechanisms underlying some specific properties of the jujube. Its high vitamin C content can be attributed to a unique high level expression of genes involved in both biosynthesis and regeneration. Our study provides insights into jujube-specific biology and valuable genomic resources for the improvement of Rhamnaceae plants and other fruit trees.


Url:
DOI: 10.1038/ncomms6315
PubMed: 25350882
PubMed Central: 4220462


Affiliations:


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<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Zhao, Jin" sort="Zhao, Jin" uniqKey="Zhao J" first="Jin" last="Zhao">Jin Zhao</name>
<affiliation wicri:level="1">
<nlm:aff id="a4">
<institution>College of Life Science, Agricultural University of Hebei</institution>
, 071000 Baoding,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Cai, Qing Le" sort="Cai, Qing Le" uniqKey="Cai Q" first="Qing-Le" last="Cai">Qing-Le Cai</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Liu, Guo Cheng" sort="Liu, Guo Cheng" uniqKey="Liu G" first="Guo-Cheng" last="Liu">Guo-Cheng Liu</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Wang, Jiu Rui" sort="Wang, Jiu Rui" uniqKey="Wang J" first="Jiu-Rui" last="Wang">Jiu-Rui Wang</name>
<affiliation wicri:level="1">
<nlm:aff id="a6">
<institution>College of Forestry, Agricultural University of Hebei</institution>
, 071000 Baoding,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Zhao, Zhi Hui" sort="Zhao, Zhi Hui" uniqKey="Zhao Z" first="Zhi-Hui" last="Zhao">Zhi-Hui Zhao</name>
<affiliation wicri:level="1">
<nlm:aff id="a1">
<institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>
, 071001 Baoding,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="a3">
<institution>Jujube Working Group, International Society for Horticultural Science, Agricultural University of Hebei</institution>
, 071001 Baoding,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Liu, Ping" sort="Liu, Ping" uniqKey="Liu P" first="Ping" last="Liu">Ping Liu</name>
<affiliation wicri:level="1">
<nlm:aff id="a1">
<institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>
, 071001 Baoding,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Dai, Li" sort="Dai, Li" uniqKey="Dai L" first="Li" last="Dai">Li Dai</name>
<affiliation wicri:level="1">
<nlm:aff id="a1">
<institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>
, 071001 Baoding,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Yan, Guijun" sort="Yan, Guijun" uniqKey="Yan G" first="Guijun" last="Yan">Guijun Yan</name>
<affiliation wicri:level="1">
<nlm:aff id="a7">
<institution>School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western Australia</institution>
, Perth, Western Australia 6009,
<country>Australia</country>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Wang, Wen Jiang" sort="Wang, Wen Jiang" uniqKey="Wang W" first="Wen-Jiang" last="Wang">Wen-Jiang Wang</name>
<affiliation wicri:level="1">
<nlm:aff id="a2">
<institution>National Engineering Research Center for Agriculture in North Mountain Area (Ministry of Science and Technology of the People’s Republic of China)</institution>
, 071000 Baoding,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Li, Xian Song" sort="Li, Xian Song" uniqKey="Li X" first="Xian-Song" last="Li">Xian-Song Li</name>
<affiliation wicri:level="1">
<nlm:aff id="a2">
<institution>National Engineering Research Center for Agriculture in North Mountain Area (Ministry of Science and Technology of the People’s Republic of China)</institution>
, 071000 Baoding,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Chen, Yan" sort="Chen, Yan" uniqKey="Chen Y" first="Yan" last="Chen">Yan Chen</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Sun, Yu Dong" sort="Sun, Yu Dong" uniqKey="Sun Y" first="Yu-Dong" last="Sun">Yu-Dong Sun</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Liu, Zhi Guo" sort="Liu, Zhi Guo" uniqKey="Liu Z" first="Zhi-Guo" last="Liu">Zhi-Guo Liu</name>
<affiliation wicri:level="1">
<nlm:aff id="a1">
<institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>
, 071001 Baoding,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Lin, Min Juan" sort="Lin, Min Juan" uniqKey="Lin M" first="Min-Juan" last="Lin">Min-Juan Lin</name>
<affiliation wicri:level="1">
<nlm:aff id="a1">
<institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>
, 071001 Baoding,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Xiao, Jing" sort="Xiao, Jing" uniqKey="Xiao J" first="Jing" last="Xiao">Jing Xiao</name>
<affiliation wicri:level="1">
<nlm:aff id="a1">
<institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>
, 071001 Baoding,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Chen, Ying Ying" sort="Chen, Ying Ying" uniqKey="Chen Y" first="Ying-Ying" last="Chen">Ying-Ying Chen</name>
<affiliation wicri:level="1">
<nlm:aff id="a1">
<institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>
, 071001 Baoding,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Li, Xiao Feng" sort="Li, Xiao Feng" uniqKey="Li X" first="Xiao-Feng" last="Li">Xiao-Feng Li</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Wu, Bin" sort="Wu, Bin" uniqKey="Wu B" first="Bin" last="Wu">Bin Wu</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Ma, Yong" sort="Ma, Yong" uniqKey="Ma Y" first="Yong" last="Ma">Yong Ma</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Jian, Jian Bo" sort="Jian, Jian Bo" uniqKey="Jian J" first="Jian-Bo" last="Jian">Jian-Bo Jian</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Yang, Wei" sort="Yang, Wei" uniqKey="Yang W" first="Wei" last="Yang">Wei Yang</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Yuan, Zan" sort="Yuan, Zan" uniqKey="Yuan Z" first="Zan" last="Yuan">Zan Yuan</name>
<affiliation wicri:level="1">
<nlm:aff id="a1">
<institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>
, 071001 Baoding,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Sun, Xue Chao" sort="Sun, Xue Chao" uniqKey="Sun X" first="Xue-Chao" last="Sun">Xue-Chao Sun</name>
<affiliation wicri:level="1">
<nlm:aff id="a6">
<institution>College of Forestry, Agricultural University of Hebei</institution>
, 071000 Baoding,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Wei, Yan Li" sort="Wei, Yan Li" uniqKey="Wei Y" first="Yan-Li" last="Wei">Yan-Li Wei</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Yu, Li Li" sort="Yu, Li Li" uniqKey="Yu L" first="Li-Li" last="Yu">Li-Li Yu</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Zhang, Chi" sort="Zhang, Chi" uniqKey="Zhang C" first="Chi" last="Zhang">Chi Zhang</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Liao, Sheng Guang" sort="Liao, Sheng Guang" uniqKey="Liao S" first="Sheng-Guang" last="Liao">Sheng-Guang Liao</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="He, Rong Jun" sort="He, Rong Jun" uniqKey="He R" first="Rong-Jun" last="He">Rong-Jun He</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Guang, Xuan Min" sort="Guang, Xuan Min" uniqKey="Guang X" first="Xuan-Min" last="Guang">Xuan-Min Guang</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Wang, Zhuo" sort="Wang, Zhuo" uniqKey="Wang Z" first="Zhuo" last="Wang">Zhuo Wang</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Zhang, Yue Yang" sort="Zhang, Yue Yang" uniqKey="Zhang Y" first="Yue-Yang" last="Zhang">Yue-Yang Zhang</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Luo, Long Hai" sort="Luo, Long Hai" uniqKey="Luo L" first="Long-Hai" last="Luo">Long-Hai Luo</name>
<affiliation wicri:level="1">
<nlm:aff id="a5">
<institution>BGI-Shenzhen</institution>
, 518083 Shenzhen,
<country>China</country>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series>
<title level="j">Nature Communications</title>
<idno type="eISSN">2041-1723</idno>
<imprint>
<date when="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc>
<textClass></textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract" xml:lang="en">
<p>The jujube (
<italic>Ziziphus jujuba</italic>
Mill.), a member of family Rhamnaceae, is a major dry fruit and a traditional herbal medicine for more than one billion people. Here we present a high-quality sequence for the complex jujube genome, the first genome sequence of Rhamnaceae, using an integrated strategy. The final assembly spans 437.65 Mb (98.6% of the estimated) with 321.45 Mb anchored to the 12 pseudo-chromosomes and contains 32,808 genes. The jujube genome has undergone frequent inter-chromosome fusions and segmental duplications, but no recent whole-genome duplication. Further analyses of the jujube-specific genes and transcriptome data from 15 tissues reveal the molecular mechanisms underlying some specific properties of the jujube. Its high vitamin C content can be attributed to a unique high level expression of genes involved in both biosynthesis and regeneration. Our study provides insights into jujube-specific biology and valuable genomic resources for the improvement of Rhamnaceae plants and other fruit trees.</p>
</div>
</front>
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<li>Australie</li>
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<name sortKey="Wei, Yan Li" sort="Wei, Yan Li" uniqKey="Wei Y" first="Yan-Li" last="Wei">Yan-Li Wei</name>
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<name sortKey="Zhang, Chi" sort="Zhang, Chi" uniqKey="Zhang C" first="Chi" last="Zhang">Chi Zhang</name>
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<name sortKey="Zhao, Zhi Hui" sort="Zhao, Zhi Hui" uniqKey="Zhao Z" first="Zhi-Hui" last="Zhao">Zhi-Hui Zhao</name>
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