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Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome

  • Jia, Kai-Hua1
  • Liu, Hui1
  • Zhang, Ren-Gang2
  • Xu, Jie1
  • Zhou, Shan-Shan1
  • Jiao, Si-Qian1
  • Yan, Xue-Mei1
  • Tian, Xue-Chan1
  • Shi, Tian-Le1
  • Luo, Hang1
  • Li, Zhi-Chao1
  • Bao, Yu-Tao1
  • Nie, Shuai1
  • Guo, Jing-Fang1
  • Porth, Ilga3
  • El-Kassaby, Yousry A.4
  • Wang, Xiao-Ru1, 5
  • Chen, Charles6
  • Van de Peer, Yves7, 8, 9, 10
  • Zhao, Wei1, 5
  • And 1 more
  • 1 Beijing Forestry University, Beijing, 100083, China , Beijing (China)
  • 2 Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang, Shandong, 261000, China , Weifang (China)
  • 3 Université Laval, Québec City, QC, G1V 0A6, Canada , Québec City (Canada)
  • 4 University of British Columbia, Vancouver, BC, V6T 1Z4, Canada , Vancouver (Canada)
  • 5 Umeå University, Umeå, SE-901 87, Sweden , Umeå (Sweden)
  • 6 Oklahoma State University, Stillwater, OK, USA , Stillwater (United States)
  • 7 Ghent University, Ghent, Belgium , Ghent (Belgium)
  • 8 VIB Center for Plant Systems Biology, Ghent, 9052, Belgium , Ghent (Belgium)
  • 9 University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa , Pretoria (South Africa)
  • 10 Nanjing Agricultural University, Nanjing, 210095, China , Nanjing (China)
Published Article
Horticulture Research
Nature Publishing Group UK
Publication Date
Sep 01, 2021
DOI: 10.1038/s41438-021-00614-y
Springer Nature
  • article


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.

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