ZhouXingLiuEtAl2019

Reference

Zhou, S.-S., Xing, Z., Liu, H., Hu, X.-G., Gao, Q., Xu, J., Jiao, S.-Q., Jia, K.-H., Jin, Y.Q., Zhao, W., Porth, I., El-Kassaby, Y.A. and Mao, J.-F. (2019) In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species' adaptability to environmental cues. BMC Genomics, 20(1). (Scopus )

Abstract

Background: Cupressus gigantea, a rare and endangered tree species with remarkable medicinal value, is endemic to the Tibetan Plateau. Yet, little is known about the underlying genetics of the unique ecological adaptability of this extremely long-lived conifer with a large genome size. Here, we present its first de novo and multi-tissue transcriptome in-depth characterization. Results: We performed Illumina paired-end sequencing and RNA libraries assembly derived from terminal buds, male and female strobili, biennial leaves, and cambium tissues taken from adult C. gigantea. In total, large-scale high-quality reads were assembled into 101,092 unigenes, with an average sequence length of 1029 bp, and 6848 unigenes (6.77%) were mapped against the KEGG databases to identify 292 pathways. A core set of 41,373 genes belonging to 2412 orthologous gene families shared between C. gigantea and nine other plants was revealed. In addition, we identified 2515 small to larger-size gene families containing in total 9223 genes specific to C. gigantea, and enriched for gene ontologies relating to biotic interactions. We identified an important terpene synthases gene family expansion with its 121 putative members. Conclusions: This study presents the first comprehensive transcriptome characterization of C. gigantea. Our results will facilitate functional genomic studies to support genetic improvement and conservation programs for this endangered conifer. © 2019 The Author(s).

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@ARTICLE { ZhouXingLiuEtAl2019,
    AUTHOR = { Zhou, S.-S. and Xing, Z. and Liu, H. and Hu, X.-G. and Gao, Q. and Xu, J. and Jiao, S.-Q. and Jia, K.-H. and Jin, Y.Q. and Zhao, W. and Porth, I. and El-Kassaby, Y.A. and Mao, J.-F. },
    TITLE = { In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species' adaptability to environmental cues },
    JOURNAL = { BMC Genomics },
    YEAR = { 2019 },
    VOLUME = { 20 },
    NUMBER = { 1 },
    NOTE = { cited By 0 },
    ABSTRACT = { Background: Cupressus gigantea, a rare and endangered tree species with remarkable medicinal value, is endemic to the Tibetan Plateau. Yet, little is known about the underlying genetics of the unique ecological adaptability of this extremely long-lived conifer with a large genome size. Here, we present its first de novo and multi-tissue transcriptome in-depth characterization. Results: We performed Illumina paired-end sequencing and RNA libraries assembly derived from terminal buds, male and female strobili, biennial leaves, and cambium tissues taken from adult C. gigantea. In total, large-scale high-quality reads were assembled into 101,092 unigenes, with an average sequence length of 1029 bp, and 6848 unigenes (6.77%) were mapped against the KEGG databases to identify 292 pathways. A core set of 41,373 genes belonging to 2412 orthologous gene families shared between C. gigantea and nine other plants was revealed. In addition, we identified 2515 small to larger-size gene families containing in total 9223 genes specific to C. gigantea, and enriched for gene ontologies relating to biotic interactions. We identified an important terpene synthases gene family expansion with its 121 putative members. Conclusions: This study presents the first comprehensive transcriptome characterization of C. gigantea. Our results will facilitate functional genomic studies to support genetic improvement and conservation programs for this endangered conifer. © 2019 The Author(s). },
    AFFILIATION = { Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China; Resources and Environmental College, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, 860000, China; Départment des Sciences du Bois et de la Forêt, Université Laval, Avenue de la Médecine, Québec, QC G1V 0A6, Canada; Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada },
    ART_NUMBER = { 213 },
    AUTHOR_KEYWORDS = { Cupressus gigantea; De novo transcriptome assembly; Ecology; Gene family evolution; Gene functional annotation },
    DOCUMENT_TYPE = { Article },
    DOI = { 10.1186/s12864-019-5584-6 },
    SOURCE = { Scopus },
    URL = { https://www.scopus.com/inward/record.uri?eid=2-s2.0-85062855406&doi=10.1186%2fs12864-019-5584-6&partnerID=40&md5=8a22b82a8da211b85a94d7550a20e998 },
}

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