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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The complex jujube genome provides insights into fruit tree biology</title><author><name sortKey="Liu, Meng Jun" sort="Liu, Meng Jun" uniqKey="Liu M" first="Meng-Jun" last="Liu">Meng-Jun Liu</name><affiliation><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></affiliation><affiliation><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></affiliation><affiliation><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></affiliation></author><author><name sortKey="Zhao, Jin" sort="Zhao, Jin" uniqKey="Zhao J" first="Jin" last="Zhao">Jin Zhao</name><affiliation><nlm:aff id="a4"><institution>College of Life Science, Agricultural University of Hebei</institution>, 071000 Baoding,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a6"><institution>College of Forestry, Agricultural University of Hebei</institution>, 071000 Baoding,<country>China</country></nlm:aff></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><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></affiliation><affiliation><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></affiliation></author><author><name sortKey="Liu, Ping" sort="Liu, Ping" uniqKey="Liu P" first="Ping" last="Liu">Ping Liu</name><affiliation><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Dai, Li" sort="Dai, Li" uniqKey="Dai L" first="Li" last="Dai">Li Dai</name><affiliation><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yan, Guijun" sort="Yan, Guijun" uniqKey="Yan G" first="Guijun" last="Yan">Guijun Yan</name><affiliation><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></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><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></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><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></affiliation></author><author><name sortKey="Chen, Yan" sort="Chen, Yan" uniqKey="Chen Y" first="Yan" last="Chen">Yan Chen</name><affiliation><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></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><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Xiao, Jing" sort="Xiao, Jing" uniqKey="Xiao J" first="Jing" last="Xiao">Jing Xiao</name><affiliation><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></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><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wu, Bin" sort="Wu, Bin" uniqKey="Wu B" first="Bin" last="Wu">Bin Wu</name><affiliation><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Ma, Yong" sort="Ma, Yong" uniqKey="Ma Y" first="Yong" last="Ma">Yong Ma</name><affiliation><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yang, Wei" sort="Yang, Wei" uniqKey="Yang W" first="Wei" last="Yang">Wei Yang</name><affiliation><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yuan, Zan" sort="Yuan, Zan" uniqKey="Yuan Z" first="Zan" last="Yuan">Zan Yuan</name><affiliation><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></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><nlm:aff id="a6"><institution>College of Forestry, Agricultural University of Hebei</institution>, 071000 Baoding,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Zhang, Chi" sort="Zhang, Chi" uniqKey="Zhang C" first="Chi" last="Zhang">Chi Zhang</name><affiliation><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Zhuo" sort="Wang, Zhuo" uniqKey="Wang Z" first="Zhuo" last="Wang">Zhuo Wang</name><affiliation><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25350882</idno><idno type="pmc">4220462</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4220462</idno><idno type="RBID">PMC:4220462</idno><idno type="doi">10.1038/ncomms6315</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000443</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The complex jujube genome provides insights into fruit tree biology</title><author><name sortKey="Liu, Meng Jun" sort="Liu, Meng Jun" uniqKey="Liu M" first="Meng-Jun" last="Liu">Meng-Jun Liu</name><affiliation><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></affiliation><affiliation><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></affiliation><affiliation><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></affiliation></author><author><name sortKey="Zhao, Jin" sort="Zhao, Jin" uniqKey="Zhao J" first="Jin" last="Zhao">Jin Zhao</name><affiliation><nlm:aff id="a4"><institution>College of Life Science, Agricultural University of Hebei</institution>, 071000 Baoding,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a6"><institution>College of Forestry, Agricultural University of Hebei</institution>, 071000 Baoding,<country>China</country></nlm:aff></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><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></affiliation><affiliation><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></affiliation></author><author><name sortKey="Liu, Ping" sort="Liu, Ping" uniqKey="Liu P" first="Ping" last="Liu">Ping Liu</name><affiliation><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Dai, Li" sort="Dai, Li" uniqKey="Dai L" first="Li" last="Dai">Li Dai</name><affiliation><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yan, Guijun" sort="Yan, Guijun" uniqKey="Yan G" first="Guijun" last="Yan">Guijun Yan</name><affiliation><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></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><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></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><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></affiliation></author><author><name sortKey="Chen, Yan" sort="Chen, Yan" uniqKey="Chen Y" first="Yan" last="Chen">Yan Chen</name><affiliation><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></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><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Xiao, Jing" sort="Xiao, Jing" uniqKey="Xiao J" first="Jing" last="Xiao">Jing Xiao</name><affiliation><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></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><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wu, Bin" sort="Wu, Bin" uniqKey="Wu B" first="Bin" last="Wu">Bin Wu</name><affiliation><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Ma, Yong" sort="Ma, Yong" uniqKey="Ma Y" first="Yong" last="Ma">Yong Ma</name><affiliation><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yang, Wei" sort="Yang, Wei" uniqKey="Yang W" first="Wei" last="Yang">Wei Yang</name><affiliation><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yuan, Zan" sort="Yuan, Zan" uniqKey="Yuan Z" first="Zan" last="Yuan">Zan Yuan</name><affiliation><nlm:aff id="a1"><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></nlm:aff></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><nlm:aff id="a6"><institution>College of Forestry, Agricultural University of Hebei</institution>, 071000 Baoding,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Zhang, Chi" sort="Zhang, Chi" uniqKey="Zhang C" first="Chi" last="Zhang">Chi Zhang</name><affiliation><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Zhuo" sort="Wang, Zhuo" uniqKey="Wang Z" first="Zhuo" last="Wang">Zhuo Wang</name><affiliation><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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><nlm:aff id="a5"><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></nlm:aff></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
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<front><journal-meta><journal-id journal-id-type="nlm-ta">Nat Commun</journal-id><journal-id journal-id-type="iso-abbrev">Nat Commun</journal-id><journal-title-group><journal-title>Nature Communications</journal-title></journal-title-group><issn pub-type="epub">2041-1723</issn><publisher><publisher-name>Nature Pub. Group</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25350882</article-id><article-id pub-id-type="pmc">4220462</article-id><article-id pub-id-type="pii">ncomms6315</article-id><article-id pub-id-type="doi">10.1038/ncomms6315</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>The complex jujube genome provides insights into fruit tree biology</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Meng-Jun</given-names></name><xref ref-type="corresp" rid="c1">a</xref><xref ref-type="aff" rid="a1">1</xref><xref ref-type="aff" rid="a2">2</xref><xref ref-type="aff" rid="a3">3</xref><xref ref-type="author-notes" rid="n1">*</xref></contrib><contrib contrib-type="author"><name><surname>Zhao</surname><given-names>Jin</given-names></name><xref ref-type="aff" rid="a4">4</xref><xref ref-type="author-notes" rid="n1">*</xref></contrib><contrib contrib-type="author"><name><surname>Cai</surname><given-names>Qing-Le</given-names></name><xref ref-type="aff" rid="a5">5</xref><xref ref-type="author-notes" rid="n1">*</xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Guo-Cheng</given-names></name><xref ref-type="aff" rid="a5">5</xref><xref ref-type="author-notes" rid="n1">*</xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Jiu-Rui</given-names></name><xref ref-type="aff" rid="a6">6</xref></contrib><contrib contrib-type="author"><name><surname>Zhao</surname><given-names>Zhi-Hui</given-names></name><xref ref-type="aff" rid="a1">1</xref><xref ref-type="aff" rid="a3">3</xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Ping</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Dai</surname><given-names>Li</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Yan</surname><given-names>Guijun</given-names></name><xref ref-type="aff" rid="a7">7</xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Wen-Jiang</given-names></name><xref ref-type="aff" rid="a2">2</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Xian-Song</given-names></name><xref ref-type="aff" rid="a2">2</xref></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Yan</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Sun</surname><given-names>Yu-Dong</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Zhi-Guo</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Lin</surname><given-names>Min-Juan</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Xiao</surname><given-names>Jing</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Ying-Ying</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Xiao-Feng</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Wu</surname><given-names>Bin</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Ma</surname><given-names>Yong</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Jian</surname><given-names>Jian-Bo</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Yang</surname><given-names>Wei</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Yuan</surname><given-names>Zan</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Sun</surname><given-names>Xue-Chao</given-names></name><xref ref-type="aff" rid="a6">6</xref></contrib><contrib contrib-type="author"><name><surname>Wei</surname><given-names>Yan-Li</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Yu</surname><given-names>Li-Li</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Chi</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Liao</surname><given-names>Sheng-Guang</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>He</surname><given-names>Rong-Jun</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Guang</surname><given-names>Xuan-Min</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Zhuo</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Yue-Yang</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Luo</surname><given-names>Long-Hai</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><aff id="a1"><label>1</label><institution>Research Center of Chinese Jujube, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></aff><aff id="a2"><label>2</label><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></aff><aff id="a3"><label>3</label><institution>Jujube Working Group, International Society for Horticultural Science, Agricultural University of Hebei</institution>, 071001 Baoding,<country>China</country></aff><aff id="a4"><label>4</label><institution>College of Life Science, Agricultural University of Hebei</institution>, 071000 Baoding,<country>China</country></aff><aff id="a5"><label>5</label><institution>BGI-Shenzhen</institution>, 518083 Shenzhen,<country>China</country></aff><aff id="a6"><label>6</label><institution>College of Forestry, Agricultural University of Hebei</institution>, 071000 Baoding,<country>China</country></aff><aff id="a7"><label>7</label><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></aff></contrib-group><author-notes><corresp id="c1"><label>a</label><email>lmj1234567@aliyun.com</email></corresp><fn id="n1"><label>*</label><p>These authors contributed equally to this work</p></fn></author-notes><pub-date pub-type="epub"><day>28</day><month>10</month><year>2014</year></pub-date><volume>5</volume><elocation-id>5315</elocation-id><history><date date-type="received"><day>21</day><month>03</month><year>2014</year></date><date date-type="accepted"><day>18</day><month>09</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2014, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights
Reserved.</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights
Reserved.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by-nc-sa/4.0/"><pmc-comment>author-paid</pmc-comment>
<license-p>This work is licensed under a Creative Commons
Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other
third party material in this article are included in the article’s
Creative Commons license, unless indicated otherwise in the credit line; if the
material is not included under the Creative Commons license, users will need to
obtain permission from the license holder to reproduce the material. To view a copy
of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc-sa/4.0/">http://creativecommons.org/licenses/by-nc-sa/4.0/</ext-link></license-p></license></permissions><abstract><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></abstract><abstract abstract-type="web-summary"><p><inline-graphic id="i1" xlink:href="ncomms6315-i1.jpg"></inline-graphic>The jujube is a major dry fruit crop in China and is commonly used for
medicinal purposes. Here the authors sequence the genome and transcriptome of the most
widely cultivated jujube cultivar, Dongzao, and highlight the genetic and molecular
basis of agronomically important jujube traits, such as vitamin C content.</p></abstract></article-meta></front><body><p>The jujube (<italic>Ziziphus jujuba</italic> Mill.) is the most economically important member of
the Rhamnaceae, a large cosmopolitan family<xref ref-type="bibr" rid="b1">1</xref><xref ref-type="bibr" rid="b2">2</xref>. It is one of the oldest
cultivated fruit trees in the world, with evidence of domestication dating back to 7,000
years ago<xref ref-type="bibr" rid="b3">3</xref>. It is native to China and is now a major dry fruit crop with
a cultivation area of 2 million ha, the main source of income for 20 million
farmers as well as a traditional herbal medicine for more than one billion people in
Asia<xref ref-type="bibr" rid="b4">4</xref>. It has been introduced into at least 47 countries from
temperate to tropical zones throughout the five continents and is becoming increasingly
popular worldwide<xref ref-type="bibr" rid="b5">5</xref><xref ref-type="bibr" rid="b6">6</xref>.</p><p>The jujube has a range of botanical and horticultural features<xref ref-type="bibr" rid="b6">6</xref> that gives
it great potential in fruit tree molecular improvement, human health protection, and the
economical development and ecological restoration of arid region. It is well-adapted to
various biotic and abiotic stresses, especially drought and salinity (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 1</xref>), and is considered an ideal
cash crop for arid and semi-arid areas where common fruits and grain/oil crops do not
grow well. Its fruit is an excellent source of vitamin C (higher than the well-known
vitamin C-rich orange and kiwifruit) and sugar (25–30%, twice as high as most
common fruits and even higher than sugarcane and sugar beet)<xref ref-type="bibr" rid="b7">7</xref> (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 2</xref>). The jujube also has
a very easy and quick flower bud differentiation (only ~7 days), a long
flowering season lasting for 2 months, a very short period of ~6 months from
planting or sowing to yielding fruits, and a very long lifecycle, even more than 1,000
productive years<xref ref-type="bibr" rid="b3">3</xref><xref ref-type="bibr" rid="b6">6</xref> (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 1</xref>).</p><p>Furthermore, jujube tree has evolved a distinct self-shoot-pruning system comprising four
types of shoot namely primary shoot, secondary shoot, mother bearing shoot (MBS) and
bearing shoot<xref ref-type="bibr" rid="b6">6</xref>, each of which has a very different function and
developmental pattern. Primary shoot is the only normally extended shoot. Secondary
shoot occurs from each node of the primary shoot and its tip dies back naturally. MBS is
the branch producing bearing shoots, it is formed at each node of the secondary shoot
and is extremely condensed elongating only ~1 mm per year. Bearing
shoot is the only fruiting shoot, it is deciduous and drops before winter normally,
which is a very uncommon trait in tree plants. This self-shoot-pruning system makes it
easy to control tree size, and the diversified shoot types offers a unique model for
elucidating shoot development and function.</p><p>Sugar and vitamin C contents are the most common indicators of fruit quality, pruning is
the most labour-consuming work of orchard management, earlier fruiting and more
productive years are what farmers expect, and drought and salinity are the main abiotic
stresses for fruit growing. Therefore, the aforementioned properties of the jujube are
of great importance to the modern fruit production characterized by fast payback, easy
management and labour-saving. In addition, the jujube is a close relative of Rosaceae
(both belonging to the Rosales order in the widely accepted molecular taxonomy system of
Angiosperm<xref ref-type="bibr" rid="b8">8</xref><xref ref-type="bibr" rid="b9">9</xref>), the most important fruit-producing family containing
a large number of leading deciduous fruit species such as apple (<italic>Malus
domestica</italic>), pear (<italic>Pyrus bretschneideri</italic>), peach (<italic>Prunus persica</italic>),
strawberry (<italic>Fragaria vesca</italic>) and <italic>Rubus</italic>. Consequently, the jujube could be a
rich source of genes for the molecular improvement of fruit trees, and a fundamental
understanding of the genetics of the jujube is crucial.</p><p>So far, more than 70 plant genomes have been sequenced and assembled since the genome
sequence of <italic>Arabidopsis thaliana</italic><xref ref-type="bibr" rid="b10">10</xref> was published in 2000. However,
high level of heterozygosity and repeated sequences and low content of GC are still the
main obstacles for genome sequencing and assembly using the next-generation-sequencing
(NGS) technology. Owing to the short read length of the NGS technology, the assembling
algorithm is always based on de Bruijn graph<xref ref-type="bibr" rid="b11">11</xref>, where heterozygous locus
between haploid becomes a bubble resulting in the breakdown of the final assembly at the
heterozygous locus. The repeated sequences make the assembly fragmental in the similar
way. Bacterial artificial chromosome-to-bacterial artificial chromosome (BAC-to-BAC)
strategy was reintroduced and a few genomes have been assembled at a reasonable
level<xref ref-type="bibr" rid="b12">12</xref><xref ref-type="bibr" rid="b13">13</xref><xref ref-type="bibr" rid="b14">14</xref>. We revealed not only both high heterozygosity and
high density of repeated sequence but also low GC content in the jujube genome, which
indicated that new method should be applied to obtain a good quality sequence for this
complex genome.</p><p>Knowledge of jujube genetics and genomics is very limited, and no genome-wide study (data
on the genome size, heterozygosity and a completed molecular genetic linkage map) on any
members of the family Rhamnaceae has so far been published, which has significantly
hindered the molecular breeding, biological research and deep utilization of the jujube.
In this research, we generate and analyze a high-quality genome sequence of one of the
oldest and most widely cultivated Chinese jujube cultivars,
‘Dongzao’ (2<italic>n</italic>=2<italic>x</italic>=24), using a novel strategy
integrating whole-genome shotgun (WGS) sequencing, BAC-to-BAC and a PCR-free library. We
also conduct comprehensive transcriptome analyses of 15 different tissues and
evolutionary comparisons with related species to identify genetic characteristics that
are likely to underpin some of the most valuable traits of jujube. Our study offers a
rich resource of genetic information for the breeding of jujube and the molecular
improvement of other Rhamnaceae plants and fruit species.</p><sec disp-level="1" sec-type="results"><title>Results</title><sec disp-level="2"><title>Sequencing and assembly of the complex jujube genome</title><p>Our analysis of the 17-mer frequency distribution based on short insert size
(<1 Kbp) clean data and simulation revealed a heterozygosity
of 1.90% in the jujube genome (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 3</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 2</xref>). This is the highest degree of heterozygosity
among the plants sequenced to date by NGS technology (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 4</xref>), which is almost twice
the second-highest level of heterozygosity in plants (1.02%, pear)<xref ref-type="bibr" rid="b14">14</xref>. In addition, the density of simple sequence repeats (SSRs) in
the jujube genome reached 378.1 SSRs per Mb, which is 2.00 times and 2.84 times
that found in its close relative species peach and apple, respectively (<xref ref-type="supplementary-material" rid="S1">Supplementary Tables 5</xref> and <xref ref-type="supplementary-material" rid="S1">6</xref>)<xref ref-type="bibr" rid="b15">15</xref><xref ref-type="bibr" rid="b16">16</xref>. The very
high level of heterozygosity, very high density of SSRs and low GC content
(33.41%) (<xref ref-type="table" rid="t1">Table 1</xref>) make the jujube genome a challenge
for the WGS strategy using NGS technology.</p><p>A strategy combining WGS sequencing, BAC-to-BAC and WGS-PCR-free library was
employed to reduce the impact of the complexity of the jujube genome. WGS was
used to construct libraries of different insert sizes, ranging from
170 bp to 40 kb (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 7</xref>). A total of 21,504 BAC clones (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 8</xref>) were selected for
sequencing at an average of 68 × coverage using the Illumina HiSeq 2000
system, representing a total of 5.86 × coverage of jujube genome size.
These BAC sequences were taken as BAC end data to overcome the heterozygosity
problem and to improve genome assembly. Paired-end-libraries of 170 to
800 bp were constructed and sequenced at 318 × coverage to
fill in the gaps. WGS mate-pair libraries of 2, 5, 10, 20 and 40 kb
were constructed and sequenced at 69 × coverage to build super
scaffolds. However, parts of the genome were missing from the sequencing data
owing to low GC content and the high density and even distribution of SSRs.
Thus, WGS-PCR-free libraries were constructed and sequenced to reduce the bias
in library construction caused by low GC content genome regions, then
30 Mb sequences were added to the final assembly. Finally, we
assembled all the above sequencing data into 28,930 contigs and 5,898 scaffolds
with N50 sizes of 33.95 kb and 301.04 kb, respectively,
spanning 437.65 Mb of the genome sequence (<xref ref-type="table" rid="t1">Table
1</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Table
9</xref>). The assembly covered 98.6% of the jujube genome
(444 Mb) estimated by our 17-mer sequence analysis (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 3</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 2</xref>). In jujube genome, the
percentage of low GC content sequences (with GC% range from 25–30%)
are much higher than that in grape vine and peach genomes (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 3</xref>).</p><p>To further evaluate the accuracy of the genome assembly, full-length sequences of
four randomly selected BACs, later demonstrated to be located in
pseudo-chromosomes 1, 2, 3 and 11 (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 4</xref>), were sequenced and assembled using Sanger
sequencing technology. Each BAC was aligned to three scaffolds at most, with an
average coverage ratio of 98.5% (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 10</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 5</xref>). In addition, our assembled sequence covered
>98.1% of the 1,942 published ESTs (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/nucest/?term%20=jujube">http://www.ncbi.nlm.nih.gov/nucest/?term =jujube</ext-link>, downloaded on
July 2013) and 97.8% of the transcriptome sequences (<xref ref-type="supplementary-material" rid="S1">Supplementary Tables 11</xref> and <xref ref-type="supplementary-material" rid="S1">12</xref>). Together, the above results indicate the
high quality of our jujube genome sequence.</p></sec><sec disp-level="2"><title>Genome sequence anchoring and pseudo-chromosome construction</title><p>To anchor the assembled genome sequences to the jujube chromosomes, we mapped the
scaffolds to a high density molecular genetic map that we constructed <italic>de
novo</italic> using an inter-specific population (105 progenies) between <italic>Z.
jujuba</italic> (female, <italic>2n</italic>=2<italic>x</italic>=24) and <italic>Z. acidojujuba</italic> (male,
<italic>2n</italic>=2<italic>x</italic>=24). Each individual in the F1 population was genotyped
by restriction site-associated DNA sequencing (RAD-Seq). Sequencing reads of
parents and the population are aligned to the jujube genome sequences using
SOAP2 (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 13</xref>). The
final map spanned 974.01 cM for the female parent and
935.40 cM for the male parent across the 12 linkage groups, with a
mean genetic distance between markers (single nucleotide polymorphisms (SNPs))
of 0.56 cM and 0.43 cM, respectively. The joint map across
the 12 linkage groups was composed of 2,419 SNP markers spanning
1,020.22 cM, with a mean marker distance of 0.42 cM.</p><p>Combining the assembled genome sequences and the genetic linkage groups, we
constructed pseudo-molecules for each of the 12 chromosomes and ordered them on
the basis of genetic length (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 4</xref>). Using the mapped markers with known sequences
that were uniquely aligned to the assembled scaffolds, a total of 1,120
scaffolds were anchored to the 12 linkage groups, comprising 73.56%
(321.45 Mb) of the jujube genome assembly (<xref ref-type="fig" rid="f1">Fig.
1</xref>). Of the anchored scaffolds, 784 could be oriented
(267.98 Mb, 83.37% of the total anchored sequences), suggesting high
alignment accordance between the anchored genetic markers and the sequenced
scaffolds.</p></sec><sec disp-level="2"><title>Genome annotation and characterization</title><p>We annotated the jujube genome by combining <italic>ab initio</italic> gene predictions,
protein-based homology searches and experimental data (RNA-Seq). A total of
32,808 protein-coding genes with an average coding sequence length of
1,190 bp and 4.5 exons per gene were predicted (<xref ref-type="supplementary-material" rid="S1">Supplementary Tables 14</xref> and <xref ref-type="supplementary-material" rid="S1">15</xref>). Overall, 78.26% of the gene models were
predicted to contain two or more exons (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 16</xref>), and 89.80% of the predicted proteins were
supported by the RNA-Seq data (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 17</xref>), showing the high accuracy of gene
annotation. In addition, we identified a total of 410 ribosomal RNAs, 1,209
transfer RNAs, 286 small nuclear RNAs and 272 microRNAs in the jujube genome
(<xref ref-type="supplementary-material" rid="S1">Supplementary Table 18</xref>).</p><p>Tissue-specific genes and housekeeping genes were also screened in our
24 Gb of RNA-Seq data from five tissues. We found that 613, 249, 382,
553 and 184 genes were specifically expressed in the root, shoot, leaf, flower
or fruit, respectively. The 16,478 genes shared by all the five tissues (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 5</xref>) accounted for
81.43% of the total recorded and 50.22% of the total predicted protein-coding
genes in the jujube genome. Among these shared genes, 1,818 were constitutively
expressed housekeeping genes (<italic>τ</italic><0.07, based on the
tissue specificity index<xref ref-type="bibr" rid="b17">17</xref>), including 102 encoding ribosomal
proteins and 21 encoding translation initiation factors (<xref ref-type="supplementary-material" rid="S1">Supplementary Data 1</xref>).</p><p>We next characterized the genome by investigating genome duplication and GC
content, gene density, repeat sequences, and SSR and SNP distribution along the
pseudo-chromosomes (<xref ref-type="fig" rid="f2">Fig. 2</xref>). We identified 4.77 million
SNPs in our jujube genome sequence. In total, 79.55% of them were anchored on
the 12 pseudo-chromosomes, and the overall polymorphism density was 11 SNPs per
kb (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 19</xref>). The
SSRs were not only present at a high density (378.1
SSRs per Mb), they were also fairly evenly distributed
(<xref ref-type="fig" rid="f2">Fig. 2a</xref>, vi). We observed large regions that
alternate between high and low gene density (<xref ref-type="fig" rid="f2">Fig. 2a</xref>, iv),
which was also noted in peach<xref ref-type="bibr" rid="b15">15</xref>. The density of repeated
sequences also reflects gene density (<xref ref-type="fig" rid="f2">Fig. 2a</xref>, iv and v).
The GC content is distributed unevenly in most pseudo-chromosomes (<xref ref-type="fig" rid="f2">Fig. 2a</xref>, iii).</p><p>We identified a total of 216.6 Mb of repeated sequences (49.49% of the
assembled genome) in the jujube genome (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 20</xref>). Among these sequences, 94.6% are
transposable elements (TEs). The majority of TEs are retrotransposons (38.03% of
the genome), whereas DNA transposons account for 8.08% of the genome. The most
abundant (64%) retrotransposons are long-terminal repeat elements, of which 37%
are Gypsy-type elements and 27% are of the Copia type (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 21</xref>). TE content in jujube
genome (46.82%), compared with its close relatives, appears to be similar to
that in mulberry (47%; ref. <xref ref-type="bibr" rid="b18">18</xref>), and higher than
that in peach (37%; ref. <xref ref-type="bibr" rid="b15">15</xref>) and <italic>P. mume</italic>(45%; ref. <xref ref-type="bibr" rid="b19">19</xref>). About 99.41% of TEs had a
divergence rate of >10% (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 6</xref>), indicating that most jujube TEs are relatively
ancient<xref ref-type="bibr" rid="b18">18</xref>.</p><p>In total, 23,996 genes (73% of the total number of annotated genes) were
allocated on the 12 pseudo-chromosomes. Self-alignment of the jujube genome
sequences based on the 23,996 gene models identified 943 paralogous gene groups
(<xref ref-type="fig" rid="f2">Fig. 2a,i</xref>), indicating that the jujube genome may
have undergone frequent inter-chromosome fusions and segmental duplication
during its evolutionary history. Interestingly, the gene blocks located in the
region from 9.20–14.68 Mb of pseudo-chromosome 1 showed
obvious synteny with all other chromosomes (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 7</xref>), while the very low SNP
density in this block (<xref ref-type="fig" rid="f2">Fig. 2a</xref>, vii) suggests that it is
highly conserved. Further analysis revealed that this block contains many genes
relating to sugar metabolism and stress tolerance (<xref ref-type="supplementary-material" rid="S1">Supplementary Data 2</xref>). Consequently, it might
be crucial for understanding the unusual characteristics of jujube.</p></sec><sec disp-level="2"><title>Genome comparison with closely related species</title><p>To estimate speciation times, we constructed a phylogenetic tree based on
single-copy genes of jujube and the seven other sequenced species of Rosales,
with <italic>A. thaliana</italic> (Brassicaceae) as the outgroup (<xref ref-type="fig" rid="f3">Fig.
3</xref>). The results suggest a speciation time of 79.9 million years ago
(Mya) for jujube and the clades of mulberry (<italic>Morus alba</italic>, Moraceae) and
<italic>Cannabis sativa</italic> (Cannabaceae), 87.2 Mya for jujube and Rosaceae
(including <italic>P. bretschneideri</italic>, <italic>M. domestica</italic>, <italic>P. mume</italic>, <italic>P.
persica</italic> and <italic>F. vesca</italic>), and 108.5 Mya for jujube and <italic>A.
thaliana</italic>. The speciation time is consistent with the origin time
inferred from the fossil records and the recent molecular estimation<xref ref-type="bibr" rid="b20">20</xref><xref ref-type="bibr" rid="b21">21</xref>. Moreover, our data showed that jujube and the clade of
<italic>M. alba</italic> and <italic>C. sativa</italic> diverged much earlier than the
divergence of <italic>M. domestica</italic> and <italic>F. vesca</italic> in Rosaceae. Consequently,
the jujube is the most ancient species among all of the sequenced species of
Rosales (<xref ref-type="fig" rid="f3">Fig. 3</xref>). This result supports that Rhamnaceae has
a long history and can be traced back to the Campanian<xref ref-type="bibr" rid="b22">22</xref><xref ref-type="bibr" rid="b23">23</xref>.
Thus, our analysis provides new insights into the phylogeny of Rosales plants on
the basis of genome-scale data.</p><p>To further analyze the evolutionary divergence of jujube and other species,
fourfold synonymous third-codon transversion (4DTv) rates were calculated (<xref ref-type="fig" rid="f2">Fig. 2b</xref>). The 4DTv value peaked at only 0.50 in jujube,
suggesting no recent whole-genome duplication occurred. The 4DTv value peaked at
0.06 and 0.50 for paralog pairs in pear, highlighting the recent whole-genome
duplication and α and β duplication in this species. The
orthologs between jujube and pear and between jujube and <italic>P. mume</italic> showed
that 4DTv value peaked at 0.32 and 0.27, respectively, indicating that the
divergence time between jujube and pear was earlier. All 4DTv values among
paralogs in jujube, pear and <italic>P. mume</italic> peaked at ~0.50,
indicating that the hexaploidy in these eudicots occurred at a similar time and
before the split of Rhamnaceae and Rosaceae.</p><p>To study the evolutionary events leading to the modern genome structure of the
jujube, we analyzed the syntenic relationships among jujube, pear and <italic>P.
mume</italic> (all belong to order Rosales). About 4,954 (jujube versus pear) and
5,722 (jujube versus <italic>P. mume</italic>) orthologous genes in the jujube genome were
selected. We then investigated the detailed orthologous chromosome-to-chromosome
relationships between these species (<xref ref-type="fig" rid="f2">Fig. 2c</xref>). The
complicated syntenic patterns, illustrated as mosaic chromosome-to-chromosome
orthologous relationships, unveiled a high degree of chromosomal evolution and
rearrangements among these three species. Even so, clear syntenies could be seen
among chromosomes of the three species, such as pseudo-chromosome 12 of jujube,
chromosome 4 of <italic>P. mume</italic> and chromosome 17 of pear. The analysis of the
synteny blocks among jujube, strawberry (<italic>F. vesca</italic>), peach (<italic>P.
persica</italic>) and grape (<italic>Vitis vinifera</italic>) indicated that the jujube
genome shares high collinearity with strawberry and peach (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 22</xref>).</p><p>To better understand jujube-specific biology, we performed comparative analyses
between the jujube genome and the other six sequenced species of Rosales (apple,
pear, peach, <italic>P. mume</italic>, strawberry and mulberry). We then screened these
genomes based on annotated genes in the public database. Of the 32,808
protein-coding genes (13,843 gene families) in the jujube genome, 1,043 gene
families are specific to jujube, and the largest number of gene clusters (11,930
families) is shared with peach (<xref ref-type="fig" rid="f4">Fig. 4a</xref>), indicating a
closer relationship between jujube and peach than between jujube and the other
species analyzed.</p><p>Expanded gene families, unique genes and genes under positive selection have
important roles in plant development and evolution. The jujube-specific gene
sets compared with apple, pear, strawberry, peach, <italic>P. mume</italic> and mulberry
were analyzed based on the KEGG orthology pathway database, to give an insight
into jujube-specific biology and adaptation. A total of 2,791 unique genes, 254
genes under positive selection and 39 expanded gene families (2,650 genes) were
found and assigned to KEGG pathways (<xref ref-type="fig" rid="f4">Fig. 4b</xref>). A further
functional characterization of the above genes revealed that most of them are
involved in energy metabolism, vitamin C metabolism, sugar-related metabolism
and secondary metabolism. This result is consistent with the special
physiological characteristics of the jujube.</p></sec><sec disp-level="2"><title>Genes involved in extreme accumulation of vitamin C in fruit</title><p>To explore the molecular mechanism underlying the high content of vitamin C (or
ascorbic acid (AsA)) in jujube fruit, we analyzed the genes encoding the key
enzymes involved in all the four known AsA biosynthesis pathways and the
recycling pathway during jujube fruit development. We found that those genes are
involved in two of the four pathways and most of them are specific to
L-galactose pathway (<xref ref-type="fig" rid="f5">Fig. 5a</xref> red part). Much fewer genes
are associated with myo-inositol pathway, suggesting which maybe a compensatory
pathway in jujube (<xref ref-type="fig" rid="f5">Fig. 5a</xref> blue part). Expression analyses
showed that GDP-D-mannose 3,5-epimerase and GDP-L-galactose phosphorylase (two
key enzymes in the <sc>L</sc>-galactose biosynthesis pathway) and
monodehydroascorbate reductase (<italic>MDHAR</italic>, the key enzyme in the AsA
recycling pathway) were expressed at continuously higher levels (<xref ref-type="fig" rid="f5">Fig. 5b</xref>).</p><p>Comparisons with the six other sequenced Rosales species at the genome level
revealed that GDP-L-galactose phosphorylase is a positively selected gene and
that <italic>MDHAR</italic> exhibits significant expansion in the jujube genome (<xref ref-type="fig" rid="f5">Fig. 5a,c</xref>). Based on the phylogenetic analysis of seven
Rosales species (including jujube) and one AsA-rich species (sweet orange,
<italic>Citrus sinensis</italic>) of the order Sapindales, we found that there are
five major <italic>MDHAR</italic> gene subfamilies, of which subfamilies V and IV are
specific to jujube and Rosaceae species, respectively (<xref ref-type="fig" rid="f5">Fig.
5c</xref>). There are eight copies in subfamily V, which are adjacently
located on two scaffolds (six in No. 402 and two in No. 627, No. 402 positioned
to pseudo-chromosome 1) in the jujube genome and likely to have been generated
by a tandem duplication. Interestingly, there is only one <italic>MDHAR</italic> copy
(subfamilies I, II and III) in the species without recent whole-genome
duplication including <italic>F. vesca</italic> (strawberry), <italic>P. persica</italic> (peach),
<italic>P. mume</italic>, <italic>M. alba</italic> (mulberry), <italic>Z. jujuba</italic> (jujube) and
<italic>C. sinensis</italic> (sweet orange), but there are two or more copies in the
species that have undergone recent whole-genome duplication, that is, <italic>M.
domestica</italic> (apple) and <italic>P. bretschneideri</italic> (pear).</p><p>Collectively, our data indicate that the L-galactose pathway is the major route
to AsA biosynthesis and that <italic>MDHAR</italic> contributes to AsA regeneration in
jujube.</p></sec><sec disp-level="2"><title>Genes involved in high level accumulation of sugar in fruit</title><p>To investigate the molecular mechanism underlying the high content of sugar in
jujube fruit, we analyzed the genomic and RNA-Seq data and the sugar contents of
fruits at four crucial development stages (young, white mature, half-red and
full red).</p><p>Our analysis showed that, fructose and glucose are the predominant sugars in
young jujube fruits, whereas in mature fruits, sucrose and total sugar content
are substantially increased, with sucrose becoming the dominant sugar (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 23</xref>). The
annotated jujube genome contains 393 genes involved in starch and sucrose
metabolism, 98 involved in galactose metabolism, 67 involved in fructose and
mannose metabolism, and 195 involved in amino sugar and nucleotide sugar
metabolism (<xref ref-type="supplementary-material" rid="S1">Supplementary Data 3</xref>).
Compared with other sequenced species of the order Rosales, all these gene
families are expanded in jujube to some extent (<xref ref-type="fig" rid="f4">Fig. 4b</xref>,
IV and V), which is consistent with the high expression patterns of these genes
in jujube fruit (<xref ref-type="fig" rid="f5">Fig. 5b</xref>). The final sugar accumulation is
determined by sugar being transported from the phloem into the fruit. We found
that the expression of most genes related to the major facilitator superfamily
sugar transporter was enhanced in parallel with jujube fruit ripening (<xref ref-type="fig" rid="f5">Fig. 5b</xref>).</p></sec><sec disp-level="2"><title>Genes involved in the distinct self-shoot-pruning system</title><p>We generated and analyzed RNA-Seq data on the four types of shoot to investigate
the genetic basis underlying jujube shoot biology (<xref ref-type="fig" rid="f6">Fig.
6</xref>). Among the four types of shoots, the number of genes differentially
expressed is the smallest between primary shoot and secondary shoot, which
indicates the similar metabolism of the two predominant shoots in vegetative
growth. The genes related to secondary metabolism, including those involved in
arginine, lipid and polyamine metabolism, were expressed at much higher levels
in these two types of shoot than in bearing shoot. These results are consistent
with the environmental suitability of different types of shoot.</p><p>In MBS, the genes involved in abscisic acid (ABA) synthesis, such as the
<italic>PYR/PYL</italic> genes, were much more highly expressed than in other shoot
types, which might be a genetic basis of the extreme slow growth of MBS and the
deciduous habit of bearing shoot attached on MBS. And the genes involved in
porphyrin and chlorophyll metabolism were dramatically downregulated in the MBS,
illustrating the decline in photosynthesis in this type of shoot.</p><p>In bearing shoot, the genes related to photosynthesis, such as those in the
light-harvesting chlorophyll binding protein gene family and those involved in
carbohydrate metabolism, were expressed at much higher levels than in all the
other three shoot types, and the genes responsive to brassinosteroids and
cytokinins were expressed at much lower levels in bearing shoots. The gene
expression profiles meet the needs of its fruiting function and deciduous
habit.</p><p>One of the more interesting things is that bearing shoots are normally deciduous,
but could become lignified and persistent (not drop in the winter) in case they
are extremely vigorous (<xref ref-type="supplementary-material" rid="S1">Supplementary
Fig. 9</xref>). The genes involved in plant hormone signal transduction were
expressed in patterns, suggesting that they play key roles in this process.
Small auxin-up RNA, cyclin D3 and two-component response regulator ARR-A family,
which are responsive to auxin, brassinosteroids and cytokinins, respectively,
were much more highly expressed in lignified bearing shoots (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 24</xref>). However, genes
responsive to ethylene and ABA, such as ABA responsive element binding factor,
serine/threonine-protein kinase SRK2 and ethylene-responsive transcription
factor 1, were more strongly expressed in deciduous bearing shoots (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 24</xref>). In
addition, genes responsive to jasmonic acid were expressed at lower levels in
deciduous bearing shoots than in persistently lignified ones (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 24</xref>), indicating weaker
stress resistance of the deciduous bearing shoot.</p></sec><sec disp-level="2"><title>Genes involved in the adaptation to abiotic/biotic stress</title><p>Gene Ontology annotation of the jujube-specific gene families showed that some of
them may take part in defence and stress responses (<xref ref-type="fig" rid="f4">Fig.
4b</xref>, XI and <xref ref-type="supplementary-material" rid="S1">Supplementary Data
4</xref>). The number of the gene families functionally annotated as
‘response to stress’ reaches up to 854. Arginine
metabolism plays an important role in plants’ perception and
adaptation to environmental disturbances, and many jujube-specific genes are
also enriched in this pathway (<xref ref-type="fig" rid="f4">Fig. 4b</xref>, VI).</p><p>The genes responding to osmotic stress are expressed at very high levels at all
stages of fruit development, which is consistent with jujube's salt tolerance
and drought resistance (<xref ref-type="supplementary-material" rid="S1">Supplementary
Table 25</xref>). Chitinases are pathogenesis related proteins that are
induced by biotic and abiotic stress in plants<xref ref-type="bibr" rid="b24">24</xref><xref ref-type="bibr" rid="b25">25</xref>. The high
expression of chitinases in jujube shoots may contribute to its high stress
tolerance (<xref ref-type="supplementary-material" rid="S1">Supplementary Table
26</xref>).</p><p>There are 13 genes encoding homologues of autophagy-related protein 9 in the
jujube genome, and only 1–2 in the other 6 related species of Rosales
(<xref ref-type="supplementary-material" rid="S1">Supplementary Table 27</xref>).
Autophagy has important roles in various cellular functions<xref ref-type="bibr" rid="b26">26</xref>.
Specifically, in immunity, the stimulation of autophagy in infected cells helps
the cells to degrade and eliminate intracellular pathogens. Therefore, autophagy
may play important roles in jujube's defence responses.</p><p>Resistance (R) proteins function mainly in biotic stress responses, and they
possess both a nucleotide-binding site (NBS) and a leucine rich repeat (LRR).
Enrichment analyses of both IntrePro domains and gene ontology terms showed that
the 849 <italic>R</italic> genes in jujube could be classified into 7 groups: CC-NBS-LRR,
CC-NBS, LRR-RLK, NBS-LRR, NBS, TIR-NBS-LRR and TIR-NBS. The CC-NBS-LRR group
(115 genes) was the most abundant among the 11 sequenced species from
diversified taxa (<xref ref-type="supplementary-material" rid="S1">Supplementary Table
28</xref>). A large number of <italic>R</italic> genes (140, 16%) are scattered
throughout chromosome 9, indicating that this chromosome is an important
candidate target for further research on disease resistance of jujube. Moreover,
17% of jujube genes with a nucleotide-binding adaptor shared by APAF-1, R
proteins and CED-4 domain are unique genes or positively selected genes, which
suggests that the function of disease resistance has been reinforced during
jujube evolution (<xref ref-type="supplementary-material" rid="S1">Supplementary Table
29</xref>).</p></sec></sec><sec disp-level="1" sec-type="discussion"><title>Discussion</title><p>High rate of heterozygosity remains a particular challenge for <italic>de novo</italic>assembly<xref ref-type="bibr" rid="b27">27</xref>. However, most perennial tree species are highly
heterozygous<xref ref-type="bibr" rid="b28">28</xref><xref ref-type="bibr" rid="b29">29</xref><xref ref-type="bibr" rid="b30">30</xref>, and it is complicated and time-consuming
to obtain their double haploid or pure line materials of very low heterozygosity.
The jujube genome was characterized as high in heterozygosity, high in density of
SSRs and low in GC content. High level of heterozygosity will fragment the assembly
of diploid genome sequenced only using the NGS technology or WGS strategy, whereas
BAC-to-BAC strategy could avoid this problem via sequencing and assembling of each
haploid BAC sequence. Due to the high SSR density and low GC content of jujube
genome, some genomic regions were missed in the WGS-PCR sequencing. To retrieve such
sequences, WGS-PCR-free library was constructed and sequenced, and 30 Mb
sequences were added to the final assembly. The finished assembly covers 98.6% of
the estimated jujube genome, >98% of the <italic>de novo</italic> transcriptome
sequence and 1,942 published ESTs, and it shows an overall identity of 98.5% with
four randomly chosen BAC sequences. Consequently, this integrated strategy provides
a good solution for assembling the complex jujube genome based on the most widely
used NGS technology nowadays.</p><p>Our genomic and RNA-Seq analyses of the jujube offers some insights into the
molecular mechanisms underlying the extreme accumulation of vitamin C and sugar in
fruit, the distinct self-shoot-pruning system and the outstanding tolerance to
abiotic/biotic stress, which are what the main breeding objectives of fruit trees.
Compared with orange and kiwifruit, two well-known vitamin C-rich fruits with
expansion and high expression of genes involved in the biosynthesis and recycling of
vitamin C (refs <xref ref-type="bibr" rid="b31">31</xref>, <xref ref-type="bibr" rid="b32">32</xref>),
respectively, the gene involved in both the biosynthesis and the recycling of
vitamin C are enhanced in jujube (<xref ref-type="fig" rid="f5">Fig. 5</xref>). This is the first
report on such a kind of accumulation mechanism of vitamin C in fruit to our
knowledge, which might elucidate why the vitamin C content of jujube is much higher
than that in orange and kiwifruit (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 2</xref>). This study indicates that the jujube would be a
useful source of genes of fruit nutrition, self-shoot-pruning and stress tolerance
for introduction into other fruit crops. To better understand and use the specific
traits of jujube, more studies should be carried out integrating further genomic and
transcriptome analysis, physiological analysis and field experiment.</p><p>The newly obtained high-quality genome sequence and gene information linked to its
valuable biological features, a relatively small genome of 444 Mb similar
to rice (466 Mb) and diploid inheritance with 12 pairs of chromosomes as
in rice, coupled with its suitable biological properties including very short
generation time, relatively small tree size, easy and quick flower bud
differentiation, long flowering season, ease of vegetative propagation and
cultivation, and a well-established <italic>in vitro</italic> regeneration system<xref ref-type="bibr" rid="b33">33</xref><xref ref-type="bibr" rid="b34">34</xref><xref ref-type="bibr" rid="b35">35</xref>, will enable the use of the jujube as a potential reference
genomic system for deciduous fruit trees.</p></sec><sec disp-level="1" sec-type="methods"><title>Methods</title><sec disp-level="2"><title>WGS sequencing and BAC sequencing</title><p>Genomic DNA was extracted from <italic>in vitro</italic> grown <italic>Z. jujuba</italic> Mill.
‘Dongzao’ plantlets. Paired-end and mate-pair Illumina WGS
libraries were constructed with multiple insert sizes (170 bp to
40 kb) according to the manufacturer’s instructions
(Illumina). For each short insert size (170, 250, 500 and 800 bp)
library construction about 5 μg genomic DNA was used, and
for large insert size (2, 5, 10, 20 and 40 Kb) library construction
20~60 μg DNA was used. Genomic DNA was
fragmented, linked to adapters and extracted at specific size after agarose gel
electrophoresis. For large insert size, first, fragments were biotin-labelled
and circularized after size selection, sheared and enriched by magnetic beads
(Invitrogen). Purified DNA was amplified by PCR, cloned to vector to yield 20
libraries for Illumina Hiseq 2000 sequencing.</p><p>We obtained 188.86 Gb raw WGS sequencing data. In the raw data
filtering process, several heuristic rules were applied: (1) we removed reads
with >2% Ns or with poly-A structure; (2) we removed reads with
≥40% low quality bases for short insert size libraries and
≥60% for large insert size libraries; (3) we removed reads containing
adapters; (4) we removed paired reads with mutual overlaps; (5) we removed PCR
duplicates. After filtering, 109.88 Gb high-quality data were
retained, representing 249.72 × genome coverage.</p><p>To overcome the key issue of high heterozygosity, high repeat content, we also
constructed BAC libraries with insert fragment size of 120 kb length.
A total of 21,504 BAC clones were randomly selected to extract plasmids. For
each clone, unique index primer and adapter index were linked to fragment end,
and a 500 bp insert size library was constructed and used for
Illumina sequencing to a coverage depth of ~5.8 × . A
pooling of 2,688 libraries (equal to 28 × 96-well plates) was sequenced
in one lane, totally 21,504 libraries were sequenced in eight lanes to generate
177.17 Gb raw data for BAC sequencing (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 8</xref>).</p></sec><sec disp-level="2"><title><italic>De novo</italic> genome assembly</title><p>The short insert size library data were corrected by correct_error programme in
the SOAPdenovo<xref ref-type="bibr" rid="b11">11</xref> software package, which changed error bases in
low frequency K-mers to form high frequency K-mers. The jujube genome was <italic>de
novo</italic> assembled using a hierarchical assembly strategy<xref ref-type="bibr" rid="b36">36</xref>along with WGS strategy. We assembled WGS sequencing data using SOAPdenovo-2.04
(ref. <xref ref-type="bibr" rid="b11">11</xref>) software with K-mer value set as 87. The
procedure included three steps: (1) construct de Bruijn graph using the short
insert size data; (2) construct scaffold by aligning reads onto the contigs and
(3) fill gaps by local assembly through mapping reads to flanking sequences of
gaps. For BAC sequencing data, we split each BAC library data by index sequences
in SOAPdenovo-2.04 (ref. <xref ref-type="bibr" rid="b11">11</xref>) software to assemble
each BAC clone. We combined the above WGS assembled sequences with the above
assembled BAC sequences based on the overlap information by Rabbit<xref ref-type="bibr" rid="b37">37</xref>, and then used the paired-end relationships of the large insert
size sequencing data to link the scaffolds/contigs into super-scaffold sequence
using SSPACE-v1.1 (ref. <xref ref-type="bibr" rid="b38">38</xref>). We filled gaps by
GapCloser v1.10 programme in the SOAPdenovo<xref ref-type="bibr" rid="b11">11</xref> software package.
To overcome the problems associated with low GC content of the jujube, PCR-free
libraries were also constructed and sequenced.</p></sec><sec disp-level="2"><title>RAD-seq for genetic map construction</title><p>The mapping population consisted of 105 inter-specific hybrids from a cross
between <italic>Z. jujuba</italic> Mill. ‘JMS2’ and <italic>Z.
acidojujuba</italic> Cheng et Liu ‘Xing 16’. Each
individual in the F1 population was genotyped with RAD-seq. The paired-end RAD
reads was mapped by SOAP2 (ref. <xref ref-type="bibr" rid="b39">39</xref>). Based on the
alignment result, the RAD-based SNP calling was done by SOAPsnp<xref ref-type="bibr" rid="b40">40</xref>. Two heterozygous SNP alleles or one heterozygous and one homozygous SNP
allele between two parents were treated as potential SNP markers if the
following criteria were satisfied: parents:sequencing depth ≥10, base
quality ≥25, copy number ≤1.5; progenies:sequencing depth
≥6, base quality ≥20, copy number ≤1.5. The
ratio of marker segregation was calculated by
<italic>χ</italic><sup>2</sup>-test. Markers showing significantly distorted
segregation (<italic>P</italic>-value < 0.01) were excluded from the map
construction. The double pseudo-test cross strategy was applied<xref ref-type="bibr" rid="b41">41</xref>. Linkage analysis was performed for markers present at least 85% using
JoinMap 4.0 software with CP population type codes<xref ref-type="bibr" rid="b42">42</xref>. An
logarithm (base 10) of odds (LOD) score of 6.0 was initially set as the linkage
threshold for linkage group identification. Twelve linkage groups that had the
same number of jujube chromosomes were formed at a LOD threshold of 6.0 and
ordered using the regression mapping algorithm. Linkage between markers,
recombination rates and map distances were calculated using the Kosambi mapping
function and the regression mapping algorithm with a recombination frequency
threshold of 0.5. The mapping position of SNP markers were first aligned to the
scaffolds and scaffolds with only one SNP marker could be anchored but not
oriented owing to a lack of markers. Finally, we scanned all SNP markers to
construct the linkage groups and to anchor scaffolds to chromosomes.</p></sec><sec disp-level="2"><title>Repeat annotation</title><p>Repetitive elements were identified by Repbase-based method<xref ref-type="bibr" rid="b43">43</xref> ,
<italic>de novo</italic> approach and TRF<xref ref-type="bibr" rid="b44">44</xref> software. We searched for
repeats using RepeatMasker<xref ref-type="bibr" rid="b45">45</xref> and RepeatProteinMask<xref ref-type="bibr" rid="b45">45</xref> software against Repbase database, identifying TEs at DNA and protein level.
Also, we employed Piler<xref ref-type="bibr" rid="b46">46</xref>, RepeatScout<xref ref-type="bibr" rid="b47">47</xref>, and
LTR-FINDER<xref ref-type="bibr" rid="b48">48</xref> programmes to build the <italic>de novo</italic> repeat
libraries and we ran RepeatMasker against the <italic>de novo</italic> library to find and
classify the repeats.</p></sec><sec disp-level="2"><title>Gene prediction</title><p>We used homology-based and <italic>de novo</italic> methods, as well as RNA-seq data, to
predict genes in the <italic>Z. jujuba</italic> genome. For homology-based gene
prediction, protein sequences from six other plant species (<italic>C. sinensis</italic>,
<italic>M. domestica</italic>, <italic>P. trichocarpa</italic>, <italic>G. max</italic>, <italic>P. persica</italic>and <italic>V. vinifera</italic>) were initially mapped onto the <italic>Z. jujuba</italic> genome
using TBLASTN<xref ref-type="bibr" rid="b49">49</xref> (<italic>E</italic>-value<1e−5), and the
homologous genome sequences were aligned against the matching proteins using
GeneWise<xref ref-type="bibr" rid="b50">50</xref> for accurate spliced alignments. Next, we used the
<italic>de novo</italic> gene prediction methods Augustus<xref ref-type="bibr" rid="b51">51</xref> and
GenScan<xref ref-type="bibr" rid="b52">52</xref>. We then integrated the homologues and those from
<italic>de novo</italic> approaches using GLEAN<xref ref-type="bibr" rid="b53">53</xref> to produce a
consensus gene set. In addition, we aligned all the RNA-seq reads to the
reference genome using TopHat<xref ref-type="bibr" rid="b54">54</xref> and predicted the open reading
frames (ORFs)s from the resulting data. Finally, we combined the GLEAN set with
the gene models produced from RNA-seq to generate a high confidence gene
set.</p><p>We did functional gene annotation by BlastP alignment to KEGG<xref ref-type="bibr" rid="b55">55</xref>,
SwissProt<xref ref-type="bibr" rid="b56">56</xref> and TrEMBL<xref ref-type="bibr" rid="b56">56</xref> databases. Motifs and
domains were determined by InterProScan<xref ref-type="bibr" rid="b57">57</xref> against protein
databases such as ProDom, PRINTS, Pfam, SMART, PANTHER and PROSITE, and Gene
Ontology<xref ref-type="bibr" rid="b58">58</xref> was obtained from the corresponding InterProScan
entries.</p></sec><sec disp-level="2"><title>Gene family clusters</title><p>The protein-coding genes from seven Rosales species
(<italic>F.
vesca</italic>, <italic>P. persica</italic>, <italic>P. mume</italic>, <italic>M. notabilis</italic>, <italic>M.
domestica</italic>, <italic>P. bretschneideri</italic> and <italic>C. sativa</italic>) and <italic>A.
thaliana</italic> were downloaded from NCBI. The longest ORF was chosen to
represent each gene, and ORF of genes encoding <50 amino acids were
filtered out. The OrthoMCL<xref ref-type="bibr" rid="b59">59</xref> method was then used to cluster all
the genes into paralogous and orthologous groups on the BLASTP alignment with
pairwise comparison strategy (<italic>E</italic>-value ≤1e−5).</p></sec><sec disp-level="2"><title>Speciation time estimation</title><p>The phylogenetic tree of eight species including jujube was constructed. The
divergence time between jujube and seven other sequenced species of Rosales
(<italic>A. thaliana</italic> as the outgroup) was estimated using MrBayes<xref ref-type="bibr" rid="b60">60</xref> and the MCMCtree programme was implemented in the Phylogenetic
Analysis by Maximum Likelihood (PAML)<xref ref-type="bibr" rid="b61">61</xref> software package.
Calibration times was obtained from the TimeTree database (<ext-link ext-link-type="uri" xlink:href="http://www.timetree.org/">http://www.timetree.org/</ext-link>).</p></sec><sec disp-level="2"><title>Transcriptome sequencing and analysis</title><p>Total RNA was extracted from 15 samples (root, primary shoot, secondary shoot,
MBS, bearing shoot, leaf, flower, young fruit, white mature fruit, half-red
fruit and full red fruit of ‘Dongzao’, deciduous and
lignified bearing shoots of ‘Dongzao’ and
‘Lizao’ (four samples)). The deciduous and lignified
bearing shoots were sampled on 26 July 2013, the stage at which we could confirm
the shoots are deciduous or lignified according to the morphological characters.
RNA-seq libraries were constructed to sequence the transcriptome of each sample.
RNA-seq libraries were sequenced on an Illumina Genome Analyzer platform. The
resulting reads were aligned to the <italic>Z. jujuba</italic> genome sequences using
TopHat<xref ref-type="bibr" rid="b54">54</xref>. After alignment, the count of mapped reads from
each sample was derived and normalized to reads per kilobase of exon per million
reads mapped for each predicted transcript using the Cufflinks<xref ref-type="bibr" rid="b54">54</xref>package. In addition to conducting the analysis described above for the <italic>Z.
jujuba</italic> transcriptome, we further assembled all reads from <italic>Z.
jujuba</italic> using the Trinity<xref ref-type="bibr" rid="b62">62</xref> package to evaluate the gene
region coverage ratio.</p></sec><sec disp-level="2"><title>Jujube-specific gene set analysis</title><p>We obtained three types of specific gene set for jujube (expansion-related genes,
positively selected genes and unique genes) from seven Rosales species (<italic>Z.
jujuba</italic>, <italic>F. vesca</italic>, <italic>P. persica</italic>, <italic>P. mume</italic>, <italic>M.
notabilis</italic>, <italic>M. domestica</italic> and <italic>P. bretschneideri</italic>).</p><p>To obtain the jujube unique gene families, we clustered gene families of the
seven sequenced Rosales plant genomes. The genes from these genomes were
collected and aligned to each other using BLASTP. Pairwise protein sequence
similarity was used as the distance for clustering genes.</p><p>To detect genes evolving under positive selection in jujube, we used gene
clustering of the seven Rosales species to identify 1,420 single-copy
orthologous genes and used the optimized branch-site model<xref ref-type="bibr" rid="b63">63</xref> to
identify 254 genes that are positively selected in <italic>Z. jujuba</italic>.</p><p>To detect expansion gene categories (SwissProt, KEGG and InterPro), we annotated
the gene functions of the seven sequenced Rosales species genes and analyzed
over-represented categories. Each domain of the three categories (SwissProt,
KEGG and InterPro) was retrieved from the seven Rosales species, and examples in
which the abundance differed between jujube and all six other species were
identified by applying Fisher’s Exact test (significance was assumed
if <italic>P</italic><0.05).</p></sec><sec disp-level="2"><title>Fruit sugar analysis</title><p>The experiment was designed as a complete randomized block with three replicates,
and four plants were used in each replicate. All samples (each 0.5 kg
fruits) were picked from <italic>Z. jujuba</italic> ‘Dongzao’ at
four developing stages including young (60 days after fruit set), white mature
(90 days after fruit set), half-red (105 days after fruit set) and full red (120
days after fruit set) in National Jujube Germplasm Repository, Taigu, China.</p><p>After drying overnight at 60 °C in the presence of silica
gel, all samples were milled to powder. For each sample, 1 g of
powder was transferred to a 50 ml volumetric flask and diluted to
40 ml with water of ultrapure grade. The flask was sonicated for
1 h at 80 °C. After cooling to room temperature,
the mixture was diluted to the volume. The extracts were filtered through filter
paper and a fraction of the filtrate was filtered through a
0.45 μm membrane filter. An HPLC system (Agilent 1200 HPLC
Series, Waldbronn, Germany) equipped with a quaternary pump system, a refractive
index detector (G1362A) was used for sucrose, glucose and fructose analysis<xref ref-type="bibr" rid="b64">64</xref>. Total sugar was determined by the anthrone method<xref ref-type="bibr" rid="b65">65</xref>. Three replicates were done for each sample and each analysis as
well.</p></sec></sec><sec disp-level="1"><title>Author contributions</title><p>M.-J.L. conceived the project. M.-J.L., J.Z. and Q.-L.C. coordinated the overall
project. G.-C.L. and Y.C. directed sequencing data generation. Q.-L.C., Y.C.,
Y.-D.S. performed the assembly. M.-J.L., J.Z., Q.-L.C., Y.C., X.-F.L., Y.-L.W. and
L.-L.Y. performed gene annotation, SNP analysis, transcriptome analysis and database
management. M.-J.L., J.Z., G.-C.L., X.-F.L. and B.W. analyzed the genome evolution.
Y.C., C.Z., G.-C.L., Y.M., X.-F.L., S.-G.L., R.-J.H. and X.-M.G. performed
repetitive elements, genome anchor, gene synteny and evolutionary analyses. M.-J.L.,
J.-RW., J.Z., J.-B.J. and W.Y. provided the materials and constructed the genetic
map. M.-J.L., J.Z., J.-RW., Z.-H.Z, P.L., L.D., Z.G.L., M.-J.Lin., J.X.,Y.-Y.C.,
Z.Y. and X.-C.S. performed sample preparation, fruit nutrition detection and data
analysis. M.-J.L. and J.Z. wrote the manuscript with contributions from Q.-L.C.,
G.-C.L., Z.-H.Z, P.L. J.-R.W., G.Y., L.D., W.-J.W., X.-S.L. and Y.C. The manuscript
was revised by M.-J.L., J.Z., G.Y., Z.W., Y.-Y.Z. and L.-H.L.</p></sec><sec disp-level="1"><title>Additional information</title><p><bold>Accession codes:</bold> The Jujube genome data has been deposited at DDBJ/EMBL/GenBank
under the accession code JREP00000000. Sequence reads of transcriptome sequencing have
been deposited in NCBI sequence read archive (SRA) under the accession code SRP046073.</p><p><bold>How to cite this article</bold>: Liu, M.-J. <italic>et al</italic>. The complex jujube
genome provides insights into fruit tree biology. <italic>Nat. Commun.</italic> 5:5315 doi:
10.1038/ncomms6315 (2014).</p></sec><sec sec-type="supplementary-material" id="S1"><title>Supplementary Material</title><supplementary-material id="d33e18" content-type="local-data"><caption><title>Supplementary Information</title><p>Supplementary Figures 1-9, Supplementary Tables 1-29 and Supplementary
References</p></caption><media xlink:href="ncomms6315-s1.pdf"></media></supplementary-material><supplementary-material id="d33e24" content-type="local-data"><caption><title>Supplementary Data 1</title><p>Housekeeping genes selected from 5 organs (τ<0.07)</p></caption><media xlink:href="ncomms6315-s2.xls"></media></supplementary-material><supplementary-material id="d33e30" content-type="local-data"><caption><title>Supplementary Data 2</title><p>The location statistics of some genes in the super-block (9.20-14.68Mb) of
LG1</p></caption><media xlink:href="ncomms6315-s3.xls"></media></supplementary-material><supplementary-material id="d33e36" content-type="local-data"><caption><title>Supplementary Data 3</title><p>Genes involved in sugar metabolism</p></caption><media xlink:href="ncomms6315-s4.xls"></media></supplementary-material><supplementary-material id="d33e42" content-type="local-data"><caption><title>Supplementary Data 4</title><p>Genes related to defense and stress responses in jujube</p></caption><media xlink:href="ncomms6315-s5.xls"></media></supplementary-material></sec></body><back><ack><p>This work was supported by grants from the National Science and Technology Support
Plan of China (2013BAD14B03), the National Natural Science Foundation of China
(31372029), the Giant Plan of Hebei, China and the Top Talent Project of Hebei,
China, and the Science Foundation for Distinguished Young Scholars of Hebei Province
(C2010000679), China. We would like to thank Dr Peter Gorsuch, MSC Scientific
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jujube.</title><p>In total, 1,120 assembled scaffolds (blue) were anchored in the 12 linkage
groups (LG1–LG12, red) using 2,213 corresponding SNP genetic
markers (grey bars). The LG numbers were assigned on the basis of the
estimated length of the genetic linkage groups.</p></caption><graphic xlink:href="ncomms6315-f1"></graphic></fig><fig id="f2"><label>Figure 2</label><caption><title>Characterization of the jujube genome, and duplication and synteny among
jujube, pear and <italic>P. mume</italic>.</title><p>(<bold>a</bold>) The genomic landscape of the 12 jujube pseudo-chromosomes. All
density information was counted in non-overlapping 200-kb windows. i,
synteny relationship of gene blocks between pseudo-chromosomes; ii,
ideograms of the 12 pseudo-chromosomes; iii, GC content density; iv, gene
density; v, repeat density, estimated by counting the repeat numbers of
non-redundant repeat annotation results; vi, SSR density and vii, SNP
density. (<bold>b</bold>) 4DTv (fourfold synonymous third-codon transversion)
value between syntenic gene pairs among the jujube, pear and <italic>P. mume</italic>.
(<bold>c</bold>) Schematic representation of syntenies among the jujube
(pseudo-chromosomes 1–12), <italic>P. mume</italic> (chromosomes
1–8) and pear genomes (chromosomes 1–17). Each line
represents a syntenic region.</p></caption><graphic xlink:href="ncomms6315-f2"></graphic></fig><fig id="f3"><label>Figure 3</label><caption><title>Estimation of divergence time between <italic>Z. jujuba</italic> and other sequenced
Rosales species.</title><p>The blue numbers on the nodes are the divergence times from the present (in
million years ago). The calibration time of the divergence of the malvids
and fabids (108–109 million years ago) is derived from He <italic>et
al</italic>.<xref ref-type="bibr" rid="b18">18</xref></p></caption><graphic xlink:href="ncomms6315-f3"></graphic></fig><fig id="f4"><label>Figure 4</label><caption><title>Jujube-specific genes.</title><p>(<bold>a</bold>) Venn diagram of orthologous gene families. Seven closely related
Rosales species (jujube, apple, pear, strawberry, peach, <italic>P. mume</italic> and
mulberry) were used to generate the Venn diagram based on the gene family
cluster analysis. The numbers in parentheses are gene families in jujube
compared with all the other six related species, and the numbers without
parentheses are those compared with the four species shown in the figure.
(<bold>b</bold>) Ratios and distributions of jujube-specific gene sets
(expansion-related genes, genes under positive selection and unique genes)
in KEGG pathways. I, biosynthesis of other secondary metabolites; II, lipid
metabolism; III, ascorbate and aldarate metabolism; IV, carbohydrate
metabolism; V, glycan biosynthesis and metabolism; VI, amino acid
metabolism; VII, nucleotide metabolism; VIII, energy metabolism; IX,
metabolism of terpenoids and polyketides; X, signal transduction; XI,
environmental adaptation; XII, cellular processes and XIII, genetic
information processing.</p></caption><graphic xlink:href="ncomms6315-f4"></graphic></fig><fig id="f5"><label>Figure 5</label><caption><title>Genes involved in sugar and AsA metabolism.</title><p>(<bold>a</bold>) The pathway involved in AsA metabolism. (<bold>b</bold>) Heat map of
RNA-Seq data for genes involved in AsA and sugar-related metabolism during
jujube fruit ripening. <italic>Y</italic>, young fruit; <italic>WM</italic>, white mature fruit;
<italic>HR</italic>, half-red fruit; <italic>FR</italic>, full red fruit. Scaled log2
expression values are shown from green to red, indicating low to high
expression. <italic>GME</italic>, GDP-D-mannose 3′,5′-epimerase;
<italic>GGP</italic>, GDP-L-galactose phosphorylase; <italic>VTC4</italic>,
inositol-phosphate phosphatase/<sc>L</sc>-galactose 1-phosphate phosphatase;
<italic>TAD</italic>, <sc>D</sc>-threo-aldose 1-dehydrogenase; <italic>Ga1LDH</italic>,
<sc>L</sc>-galactono-1,4-lactone dehydrogenase; <italic>MDHAR</italic>,
monodehydroascorbate reductase (NADH); <italic>AO</italic>, <sc>L</sc>-ascorbate
oxidase; <italic>AP</italic>, <sc>L</sc>-ascorbate peroxidase; <italic>MIOX</italic>, inositol
oxygenase; <italic>XET</italic>, xyloglucan:xyloglucosyl transferase; <italic>PE</italic>,
pectinesterase; <italic>BGluc</italic>, beta-glucosidase; <italic>BG2</italic>, beta-1,3-glucanase 2; <italic>GALE</italic>,
UDP-glucose 4-epimerase; <italic>SPS</italic>, sucrose-phosphate synthase;
<italic>SUS2</italic>, sucrose synthase; FBA, fructose-bisphosphate aldolase;
<italic>GFS</italic>, GDP-<sc>L</sc>-fucose synthase; <italic>PFP</italic>,
pyrophosphate-fructose-6-phosphate 1-phosphotransferase; <italic>PGM</italic>,
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase; <italic>PDC</italic>,
pyruvate decarboxylase; <italic>PGK</italic>, phosphoglycerate kinase; <italic>ALDH</italic>,
aldehyde dehydrogenase family 7 member A1; <italic>OT</italic>,
oligosaccharyltransferase complex subunit gamma; <italic>RFS</italic>, raffinose
synthase; <italic>NRS/ER</italic>, 3,5-epimerase/4-reductase; <italic>AXS2</italic>,
UDP-apiose/xylose synthase; <italic>UGT</italic>, UDP-glucosyltransferase;
<italic>CesA</italic>, cellulose synthase A; <italic>MFS</italic>, MFS transporter. (<bold>c</bold>)
Upper part, phylogenetic analysis of the <italic>MDHAR</italic> gene family in jujube
and seven related species; Lower part, the location of eight MDHAR genes in
two scaffolds.</p></caption><graphic xlink:href="ncomms6315-f5"></graphic></fig><fig id="f6"><label>Figure 6</label><caption><title>Heat map of the normalized RNA-Seq data for genes involved in shoot
development.</title><p><italic>P</italic>, primary shoot; <italic>S</italic>, secondary shoot; <italic>M</italic>, mother bearing
shoot; <italic>B</italic>, bearing shoot. Scaled log2 expression values are shown from
green to red, indicating low to high expression, respectively. <italic>LHC</italic>,
light-harvesting complex; <italic>FDA</italic>, fructose-bisphosphate aldolase;
<italic>MATE</italic>, multidrug resistance protein; <italic>CTK</italic>, cytokinin
receptor; <italic>MYC2</italic>, transcription factor MYC2; <italic>SRK2</italic>,
serine/threonine-protein kinase SRK2; <italic>CNS</italic>, chitinase; <italic>JAZ</italic>,
jasmonate ZIM domain-containing protein; <italic>CDPK</italic>, calcium-dependent
protein kinase; <italic>GID</italic>, gibberellin receptor; <italic>BRI</italic>, protein
brassinosteroid insensitive; <italic>DELLA</italic>, DELLA protein; <italic>IAA</italic>,
auxin-responsive protein; <italic>PYR/PYL</italic>, abscisic acid receptor PYR/PYL
family; <italic>SAGT</italic>, pathogen-inducible salicylic acid glucosyltransferase;
<italic>ETR</italic>,
ethylene receptor;
<italic>PP2C</italic>, protein phosphatase 2C; <italic>CTR1</italic>,
serine/threonine-protein kinase CTR1; <italic>JAR</italic>, jasmonic acid-amino
synthetase; <italic>UGT</italic>, UDP-glucosyltransferase; <italic>CA</italic>,
Ca<sup>2+</sup>-transporting ATPase; <italic>SAUR</italic>, SAUR family
protein; <italic>WRKY</italic>, WRKY transcription factor; <italic>CYCD3</italic>, cyclin D3;
ARR-A, two-component response regulator; <italic>FLS2</italic>, LRR receptor-like
serine/threonine-protein kinase FLS2; <italic>BG</italic>, beta-glucosidase. The
figures on the right indicate different types of shoot.</p></caption><graphic xlink:href="ncomms6315-f6"></graphic></fig><table-wrap position="float" id="t1"><label>Table 1</label><caption><title>Statistics of assembly and annotation for the jujube genome.</title></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="center"></col></colgroup><tbody valign="top"><tr><td align="left" valign="top" charoff="50"><bold>Chromosome number (2<italic>n</italic>)</bold></td><td align="center" valign="top" charoff="50"><bold>24</bold></td></tr><tr><td align="left" valign="top" charoff="50">Estimate of genome size</td><td align="center" valign="top" charoff="50">443,931,860 bp</td></tr><tr><td align="left" valign="top" charoff="50">Number of scaffolds (≥100 bp)</td><td align="center" valign="top" charoff="50">5,898</td></tr><tr><td align="left" valign="top" charoff="50">Total size of assembled scaffolds</td><td align="center" valign="top" charoff="50">437,645,007 bp</td></tr><tr><td align="left" valign="top" charoff="50">N50 (scaffolds)</td><td align="center" valign="top" charoff="50">301,045 bp</td></tr><tr><td align="left" valign="top" charoff="50">Longest scaffold</td><td align="center" valign="top" charoff="50">3,141,199 bp</td></tr><tr><td align="left" valign="top" charoff="50">Number of contigs (≥100 bp)</td><td align="center" valign="top" charoff="50">28,930</td></tr><tr><td align="left" valign="top" charoff="50">Total size of assembled contigs</td><td align="center" valign="top" charoff="50">417,332,479 bp</td></tr><tr><td align="left" valign="top" charoff="50">N50 (contigs)</td><td align="center" valign="top" charoff="50">33,948 bp</td></tr><tr><td align="left" valign="top" charoff="50">Longest contig</td><td align="center" valign="top" charoff="50">334,926 bp</td></tr><tr><td align="left" valign="top" charoff="50">GC content</td><td align="center" valign="top" charoff="50">33.41%</td></tr><tr><td align="left" valign="top" charoff="50">Number of gene models</td><td align="center" valign="top" charoff="50">32,808</td></tr><tr><td align="left" valign="top" charoff="50">Mean transcript length</td><td align="center" valign="top" charoff="50">3,799.94 bp</td></tr><tr><td align="left" valign="top" charoff="50">Mean coding sequence length</td><td align="center" valign="top" charoff="50">1,190.50 bp</td></tr><tr><td align="left" valign="top" charoff="50">Mean number of exons per gene</td><td align="center" valign="top" charoff="50">4.50</td></tr><tr><td align="left" valign="top" charoff="50">Mean exon length</td><td align="center" valign="top" charoff="50">264.40 bp</td></tr><tr><td align="left" valign="top" charoff="50">Mean intron length</td><td align="center" valign="top" charoff="50">702.43 bp</td></tr><tr><td align="left" valign="top" charoff="50">Number of predicted miRNA genes</td><td align="center" valign="top" charoff="50">272</td></tr><tr><td align="left" valign="top" charoff="50">Total size of TEs</td><td align="center" valign="top" charoff="50">204,918,483 bp</td></tr><tr><td align="left" valign="top" charoff="50">TEs share in genome</td><td align="center" valign="top" charoff="50">46.82%</td></tr></tbody></table><table-wrap-foot><fn id="t1-fn1"><p>miRNA, microRNA; TEs, transposable elements.</p></fn></table-wrap-foot></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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