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.
Highlights
Introduction Lamiaceae orLabiatae, or the mint family, is one of the largest families within the flowering plants, with 236 genera and more than 7000 species[1]
We identified a total of 88,489 gene models, including 56,267 protein-coding genes, 28,993 long noncoding RNAs, 1541 transfer RNAs, Fig. 1 Synteny and distribution of features in the S. splendens genome
When comparing S. splendens to other Lamiales species with respect to long terminal repeat (LTR)-RT accumulation and removal rates, we found that the S. splendens was characterized by large numbers of intact, solo, and truncated long terminal repeat retrotransposons (LTR-RTs) and relatively low removal rates (Supplementary Fig. 37)
Summary
An elite tetraploid S. splendens cultivar, “aoyunshenghuo (Olympic flame),” developed through multiple rounds of selfing, was selected for sequencing. For gene categories such as those detailed above (SCyes_SDyes; SCyes_SDno; SCno_SDyes; and SCno_SDno), no significant differences were found (Fig. 3b) These results indicate that TEs affect the homoeologous expression bias pattern between homoeologous chromosomes. Dynamic homoeologs had a significantly higher Ka, Ks, and Ka/Ks ratio, indicating that they have relaxed selection pressure (Fig. 4g–i) These results indicate that spatiotemporal expression patterns are positively correlated with differences in flanking TEs, cis-regulatory elements, coding sequences, and selection pressure. These observed changes in spatiotemporal expression patterns, as well as the relaxation of selection pressure, the proximity of TE and the difference of TF binding sites, may lead to functional innovation through sub- or neofunctionalization, following, for instance, divergence of gene expression. The “divergent” expression patterns in different modules foreshadow sub- or neofunctionalization between homoeologs[34]
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