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

Kai-Hua Jia, Hui Liu, Ren-Gang Zhang, Jie Xu, Shan-Shan Zhou, Si-Qian Jiao, Xue-Mei Yan, Xue-Chan Tian, Tian-Le Shi, Hang Luo, et al.
(2021) HORTICULTURE RESEARCH. 8(1).
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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 gamma 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.
Keywords
Horticulture, Plant Science, Genetics, Biochemistry, Biotechnology, TRANSPOSABLE ELEMENTS, GENE DUPLICATION, SEQUENCE, ANNOTATION, ANCIENT, POLYPLOIDY, DIVERSIFICATION, IDENTIFICATION, CONSEQUENCES, DIVERGENCE

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MLA
Jia, Kai-Hua, et al. “Chromosome-Scale Assembly and Evolution of the Tetraploid Salvia Splendens (Lamiaceae) Genome.” HORTICULTURE RESEARCH, vol. 8, no. 1, 2021, doi:10.1038/s41438-021-00614-y.
APA
Jia, K.-H., Liu, H., Zhang, R.-G., Xu, J., Zhou, S.-S., Jiao, S.-Q., … Mao, J.-F. (2021). Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome. HORTICULTURE RESEARCH, 8(1). https://doi.org/10.1038/s41438-021-00614-y
Chicago author-date
Jia, Kai-Hua, Hui Liu, Ren-Gang Zhang, Jie Xu, Shan-Shan Zhou, Si-Qian Jiao, Xue-Mei Yan, et al. 2021. “Chromosome-Scale Assembly and Evolution of the Tetraploid Salvia Splendens (Lamiaceae) Genome.” HORTICULTURE RESEARCH 8 (1). https://doi.org/10.1038/s41438-021-00614-y.
Chicago author-date (all authors)
Jia, Kai-Hua, Hui Liu, Ren-Gang Zhang, Jie Xu, Shan-Shan Zhou, Si-Qian Jiao, Xue-Mei Yan, Xue-Chan Tian, Tian-Le Shi, Hang Luo, Zhi-Chao Li, Yu-Tao Bao, Shuai Nie, Jing-Fang Guo, Ilga Porth, Yousry A. El-Kassaby, Xiao-Ru Wang, Charles Chen, Yves Van de Peer, Wei Zhao, and Jian-Feng Mao. 2021. “Chromosome-Scale Assembly and Evolution of the Tetraploid Salvia Splendens (Lamiaceae) Genome.” HORTICULTURE RESEARCH 8 (1). doi:10.1038/s41438-021-00614-y.
Vancouver
1.
Jia K-H, Liu H, Zhang R-G, Xu J, Zhou S-S, Jiao S-Q, et al. Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome. HORTICULTURE RESEARCH. 2021;8(1).
IEEE
[1]
K.-H. Jia et al., “Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome,” HORTICULTURE RESEARCH, vol. 8, no. 1, 2021.
@article{8721909,
  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 gamma 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.}},
  articleno    = {{177}},
  author       = {{Jia, Kai-Hua and Liu, Hui and Zhang, Ren-Gang and Xu, Jie and Zhou, Shan-Shan and Jiao, Si-Qian and Yan, Xue-Mei and Tian, Xue-Chan and Shi, Tian-Le and Luo, Hang and Li, Zhi-Chao and Bao, Yu-Tao and Nie, Shuai and Guo, Jing-Fang and Porth, Ilga and El-Kassaby, Yousry A. and Wang, Xiao-Ru and Chen, Charles and Van de Peer, Yves and Zhao, Wei and Mao, Jian-Feng}},
  issn         = {{2662-6810}},
  journal      = {{HORTICULTURE RESEARCH}},
  keywords     = {{Horticulture,Plant Science,Genetics,Biochemistry,Biotechnology,TRANSPOSABLE ELEMENTS,GENE DUPLICATION,SEQUENCE,ANNOTATION,ANCIENT,POLYPLOIDY,DIVERSIFICATION,IDENTIFICATION,CONSEQUENCES,DIVERGENCE}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{15}},
  title        = {{Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome}},
  url          = {{http://doi.org/10.1038/s41438-021-00614-y}},
  volume       = {{8}},
  year         = {{2021}},
}
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