JiaLiuZhangEtAl2021

Reference

Jia, K.-H., Liu, H., Zhang, R.-G., Xu, J., Zhou, S.-S., Jiao, S.-Q., Yan, X.-M., Tian, X.-C., Shi, T.-L., Luo, H., Li, Z.-C., Bao, Y.-T., Nie, S., Guo, J.-F., Porth, I., El-Kassaby, Y.A., Wang, X.-R., Chen, C., Van de Peer, Y., Zhao, W., Mao, J.-F. (2021) Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome. Horticulture Research, 8(1). (Scopus )

Abstract

Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species. © 2021, The Author(s).

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@ARTICLE { JiaLiuZhangEtAl2021,
    AUTHOR = { Jia, K.-H. and Liu, H. and Zhang, R.-G. and Xu, J. and Zhou, S.-S. and Jiao, S.-Q. and Yan, X.-M. and Tian, X.-C. and Shi, T.-L. and Luo, H. and Li, Z.-C. and Bao, Y.-T. and Nie, S. and Guo, J.-F. and Porth, I. and El-Kassaby, Y.A. and Wang, X.-R. and Chen, C. and Van de Peer, Y. and Zhao, W. and Mao, J.-F. },
    JOURNAL = { Horticulture Research },
    TITLE = { Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome },
    YEAR = { 2021 },
    NOTE = { cited By 0 },
    NUMBER = { 1 },
    VOLUME = { 8 },
    ABSTRACT = { Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species. © 2021, 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; Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang, Shandong 261000, China; Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec City, QC G1V 0A6, Canada; Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå, SE-901 87, Sweden; Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 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; College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China },
    ART_NUMBER = { 177 },
    DOCUMENT_TYPE = { Article },
    DOI = { 10.1038/s41438-021-00614-y },
    SOURCE = { Scopus },
    URL = { https://www.scopus.com/inward/record.uri?eid=2-s2.0-85114136706&doi=10.1038%2fs41438-021-00614-y&partnerID=40&md5=8fdb5d9a4fd3dd3740d453a16c33d566 },
}

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