Dataset Information

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

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.

SUBMITTER: Jia KH

PROVIDER: S-EPMC8408255 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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

Jia Kai-Hua KH Liu Hui H Zhang Ren-Gang RG Xu Jie J Zhou Shan-Shan SS Jiao Si-Qian SQ Yan Xue-Mei XM Tian Xue-Chan XC Shi Tian-Le TL Luo Hang H Li Zhi-Chao ZC Bao Yu-Tao YT Nie Shuai S Guo Jing-Fang JF Porth Ilga I El-Kassaby Yousry A YA Wang Xiao-Ru XR Chen Charles C Van de Peer Yves Y Zhao Wei W Mao Jian-Feng JF

Horticulture research 20210901 1

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, g ...[more]

PMID: 34465761

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Project description:BackgroundAs an important perennial herbaceous flower, Salvia splendens possesses high ornamental value. Understanding its branching processes may help scientists select the best plant type. Although Salvia splendens is a frequently-used horticultural flower, only limited transcriptomic or genomic research is available in public databases. In the present study, we, for the first time, constructed a comprehensive dataset for Salvia splendens through de novo high-throughput transcriptome sequencing.Methodology/principal findingsWe performed de novo transcriptome sequencing on two different branching type plants (Strain 35 and Cailinghong) using the Illumina paired-end sequencing technology. For Strain 35, a total of 16,488,829 reads were generated and assembled into 38,498 unigenes, with a mean length of approximately 779 bp. For Cailinghong, 16,464,713 reads were generated and assembled into 34,302 unigenes, with a mean length of approximately 812 bp. Moreover, a total of 49,310 unigenes for Salvia splendens were identified, among them 33,925 (68.80%) were annotated in the non-redundant NCBI database, 25,371 (51.45%) were annotated in the Swiss-Prot database, while 24,888 (50.47%) and 9,896 (20.07%) unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Using the Kyoto Encyclopedia of Genes and Genomes pathway database, we identified 134 differently expressed unigenes between Strain 35 and Cailinghong, and then these unigenes were mapped to 79 pathways. In addition, we detected 2,453 simple sequence repeats (SSRs).ConclusionsWe obtained a comprehensive transcriptomic information from this work and provided a valuable resource of transcript sequences of Salvia splendens in public databases. Moreover, some candidate genes potentially involved in branching were identified. Furthermore, numerous obtained SSRs might contribute to marker-assisted selection. These data could be further utilized in functional genomics studies on Salvia splendens.

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Dataset Information

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

Publications

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

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