Patterns of base chromosome numbers, genome size and rDNA loci evolution in the genus Capsicum (Solanaceae)

The size, organization and dynamics of the evolution of plant genomes vary widely among and within evolutionary lineages. The relatively small genus Capsicum provides an excellent system for studying genome evolution because all the species are diploid and possess one of two base chromosome numbers (x = 12 or 13). Here, we report chromosome numbers, genome sizes, and numbers of 5S and 35S rDNA loci for 24 Capsicum taxa representing eight of the nine currently recognized clades and one outgroup species, Lycianthes rantonnetii. The size of the analyzed genomes ranged from 1.66 to 7.79 pg/1C (approximately 4.6-fold variation) despite the complete absence of polyploidy. Ancestral state reconstruction based on a RADseq phylogeny inferred a relatively small ancestral genome size (~2.3 pg/1C) for the most recent common ancestor of Capsicum, followed by several independent genome expansions and contractions in individual lineages resulting in remarkable genome size uniformity within present-day clades. In the absence of polyploidy, the extent of genome size variation can be attributed to differences in repeatome dynamics. All taxa possessed a single 5S rDNA locus, but the number of 35S rDNA loci varied from one to 18, with signals differing in size and potentially only some loci representing active, intact coding arrays of rDNA monomers. A single major 35S rDNA locus was reconstructed as the ancestral state, followed predominantly by independent increases to two or three major active loci in different lineages. Differences in 35S rDNA loci appearance suggested that the minor signals might represent rDNA-derived tandem repeats, and that 35S rDNA monomers might have independently given rise to novel tandem repeats in different evolutionary lineages of the genus. The ancestral base chromosome number was inferred as x = 12, with two independent events of ascending dysploidy (x = 12 → 13) during the diversification of two derived, non-sister clades. These findings demonstrate that the evolution of genome size and base chromosome number differs in Capsicum, and that major genomic changes coincided with the origin of major clades rather than with the subsequent speciation within the lineages, resulting in strong genomic uniformity within clades.