Abstract
Key messageComparative transcriptome analysisof wild and cultivated chrysanthemums provides valuablegenomic resources and helps uncover common anddivergent patterns of genome and gene evolution in these species.Plants are unique in that they employ polyploidy (or whole-genome duplication, WGD) as a key process for speciation and evolution. The Chrysanthemum genus is closely associated with hybridization and polyploidization, with Chrysanthemum species exhibiting diverse ploidy levels. The commercially important species, C. morifolium is an allohexaploid plant that is thought to have originated via the hybridization of several Chrysanthemum species, but the genomic and molecular evolutionary mechanisms remain poorly understood. In the present study, we sequenced and compared the transcriptomes of C. morifolium and the wild Korean diploid species, C. boreale. De novo transcriptome assembly revealed 11,318 genes in C. morifolium and 10,961 genes in C. boreale, whose functions were annotated by homology searches. An analysis of synonymous substitution rates (Ks) of paralogous and orthologous genes suggested that the two Chrysanthemum species commonly experienced the Asteraceae paleopolyploidization and recent genome duplication or triplication before the divergence of these species. Intriguingly, C. boreale probably underwent rapid diploidization, with a reduction in chromosome number, whereas C. morifolium maintained the original chromosome number. Analysis of the ratios of non-synonymous to synonymous nucleotide substitutions (Ka/Ks) between orthologous gene pairs indicated that 107 genes experienced positive selection, which may have been crucial for the adaptation, domestication, and speciation of Chrysanthemum.
Highlights
Electronic supplementary material The online version of this article contains supplementary material, which is available to authorized users.The genus Chrysanthemum shows considerable diversity in terms of ploidy level, as well as flower shape, color, and size
De novo assembly of preprocessed reads resulted in the identification of 10,961 isogroups containing 13,841 isotigs for C. boreale and 11,318 isogroups containing 16,769 isotigs for C. morifolium (Table 1)
Isotigs from the two species showed similar length distributions, with an average length of 1216 bp for C. boreale and 1230 bp for C. morifolium, the number of obtained isotigs was greater in C. morifolium than in C. boreale (Fig. 1; Table 1)
Summary
The genus Chrysanthemum shows considerable diversity in terms of ploidy level, as well as flower shape, color, and size. This genus comprises approximately 40 species that exhibit various degrees of polyploidy, from diploid to decaploid, with nine chromosomes as the basal unit (Dowrick 1952; Liu et al 2012). Cytogenetic, molecular phylogenetic, and genetic studies suggested that C. morifolium originated from the natural hybridization of species such as C. indicum, C. lavandulifolium, C. nankingense, C. vestitum, and C. zawadskii (Chen 1985; Dai et al 1998, 2005; Ma et al 2016; Zhou and Silan 2001).
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