Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome. Jia, K., Liu, H., Zhang, R., Xu, J., Zhou, S., Jiao, S., Yan, X., Tian, X., Shi, T., Luo, H., Li, Z., Bao, Y., Nie, S., Guo, J., Porth, I., El-Kassaby, Y. A., Wang, X., Chen, C., Van de Peer, Y., Zhao, W., & Mao, J. Horticulture Research, 8(1):1–15, September, 2021. ![Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex 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.
@article{jia_chromosome-scale_2021,
title = {Chromosome-scale assembly and evolution of the tetraploid {Salvia} splendens ({Lamiaceae}) genome},
volume = {8},
copyright = {2021 The Author(s)},
issn = {2052-7276},
url = {https://www.nature.com/articles/s41438-021-00614-y},
doi = {10/gmskmf},
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.},
language = {en},
number = {1},
urldate = {2021-09-02},
journal = {Horticulture Research},
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},
month = sep,
year = {2021},
pages = {1--15},
}
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