Comparative transcriptome analysis reveals whole-genome duplications and gene selection patterns in cultivated and wild <i>Chrysanthemum</i> species

다국어 초록 (Multilingual Abstract)

<P><B>Key message</B></P><P>Comparative transcriptome analysis of wild and cultivated chrysanthemums provides valuable genomic resources and helps uncover common and divergent patterns of genome and gene evolution in these species.</P><P><B>Abstract</B></P><P>Plants are unique in that they employ polyploidy (or whole-genome duplication, WGD) as a key process for speciation and evolution. The <I>Chrysanthemum</I> genus is closely associated with hybridization and polyploidization, with <I>Chrysanthemum</I> species exhibiting diverse ploidy levels. The commercially important species, <I>C. morifolium</I> is an allohexaploid plant that is thought to have originated via the hybridization of several <I>Chrysanthemum</I> species, but the genomic and molecular evolutionary mechanisms remain poorly understood. In the present study, we sequenced and compared the transcriptomes of <I>C. morifolium</I> and the wild Korean diploid species, <I>C. boreale</I>. De novo transcriptome assembly revealed 11,318 genes in <I>C. morifolium</I> and 10,961 genes in <I>C. boreale</I>, whose functions were annotated by homology searches. An analysis of synonymous substitution rates (Ks) of paralogous and orthologous genes suggested that the two <I>Chrysanthemum</I> species commonly experienced the Asteraceae paleopolyploidization and recent genome duplication or triplication before the divergence of these species. Intriguingly, <I>C. boreale</I> probably underwent rapid diploidization, with a reduction in chromosome number, whereas <I>C. morifolium</I> 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 <I>Chrysanthemum</I>.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1007/s11103-017-0663-z) contains supplementary material, which is available to authorized users.</P>