XuLiuZhouEtAl2019

Reference

Xu, C.-Q., Liu, H., Zhou, S.-S., Zhang, D.-X., Zhao, W., Wang, S., Chen, F., Sun, Y.-Q., Nie, S., Jia, K.-H., Jiao, S.-Q., Zhang, R.-G., Yun, Q.-Z., Guan, W., Wang, X., Gao, Q., Bennetzen, J.L., Maghuly, F., Porth, I., de Peer, Y.V., Wang, X.-R., Ma, Y. and Mao, J.-F. (2019) Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. GigaScience, 8(2). (Scopus )

Abstract

BACKGROUND: Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. FINDINGS: We generated 51 Gb and 135 Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10× Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51 Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10× Genomics reads. Identified repeats constituted ∼82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail. CONCLUSIONS: Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis. © The Author(s) 2019. Published by Oxford University Press.

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@ARTICLE { XuLiuZhouEtAl2019,
    AUTHOR = { Xu, C.-Q. and Liu, H. and Zhou, S.-S. and Zhang, D.-X. and Zhao, W. and Wang, S. and Chen, F. and Sun, Y.-Q. and Nie, S. and Jia, K.-H. and Jiao, S.-Q. and Zhang, R.-G. and Yun, Q.-Z. and Guan, W. and Wang, X. and Gao, Q. and Bennetzen, J.L. and Maghuly, F. and Porth, I. and de Peer, Y.V. and Wang, X.-R. and Ma, Y. and Mao, J.-F. },
    TITLE = { Genome sequence of Malania oleifera, a tree with great value for nervonic acid production },
    JOURNAL = { GigaScience },
    YEAR = { 2019 },
    VOLUME = { 8 },
    NUMBER = { 2 },
    NOTE = { cited By 0 },
    ABSTRACT = { BACKGROUND: Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. FINDINGS: We generated 51 Gb and 135 Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10× Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51 Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10× Genomics reads. Identified repeats constituted ∼82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail. CONCLUSIONS: Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis. © The Author(s) 2019. Published by Oxford University Press. },
    AFFILIATION = { Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China; College of Life Science, Datong University, Datong, Shanxi 037009, China; Yunnan Key Laboratory of Forest Plant Cultivation and Utilization, State Forestry Administration Key Laboratory of Yunnan Rare and Endangered Species Conservation and Propagation, Yunnan Academy of Forestry, Kunming, Yunnan 650201, China; Yunnan Academy of ForestryYunnan, China; Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China; Department of Genetics, University of Georgia, Athens, GA 30602, United States; Plant Biotechnology Unit (PBU), Dept. Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, 1190, Austria; Département des sciences du bois et de la forêt, Université Laval, Avenue de la MédecineQuébec (Québec) G1V 0A6 1030, Canada; Institute for System and Integrated Biology, Pavillon Charles-Eugène-Marchand, Université Laval, Avenue de la MédecineQuébec (Québec) G1V 0A6 1030, Canada; Centre d'Étude de la Forêt, Université Laval, Avenue de la MédecineQuébec (Québec) G1V 0A6 1030, Canada; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium; VIB Center for Plant Systems Biology, Ghent, 9052, Belgium; Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology Genetics, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa; Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå SE-901 87, Sweden; Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China },
    AUTHOR_KEYWORDS = { de novo genome assembly; Malania; nervonic acid; transcriptomes; vulnerable plant },
    DOCUMENT_TYPE = { Article },
    DOI = { 10.1093/gigascience/giy164 },
    SOURCE = { Scopus },
    URL = { https://www.scopus.com/inward/record.uri?eid=2-s2.0-85061607772&doi=10.1093%2fgigascience%2fgiy164&partnerID=40&md5=717cb880ad7d4b57f7c3f71ecb4c8e27 },
}

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