Genome relationships and LTR-retrotransposon diversity in three cultivated Capsicum  L. (Solanaceae) species

Abstract

Background: Plant genomes are rich in repetitive sequences, and transposable elements (TEs) are the most accumulated of them. This mobile fraction can be distinguished as Class I (retrotransposons) and Class II (transposons). Retrotransposons that are transposed using an intermediate RNA and that accumulate in a “copy-and-paste” manner have been screened in three completely sequenced genomes of peppers (Solanaceae family). The goal of this study was to understand the genome relationships among Capsicum annuum , C. chinense and C. baccatum , based on a comparative analysis of the function, diversity and the chromosome distribution of TE lineages in the Capsicum karyotypes. Due to the great commercial importance of pepper in natura , as a spice or as an ornamental plant, these genomes have been widely sequenced, and all of the assemblies are available in the SolGenomics group. These sequences have been used to compare all repetitive fractions from a cytogenomic point of view. Results: The qualification and quantification of LTR-retrotransposons (LTR-RT) families are contrasted with molecular cytogenetics data, and the results show a strong genome similarity between C. annuum and C. chinense as compared to C. baccatum . The Gypsy superfamily is more abundant than Copia , especially for Tekay/Del family members, including a high representation in C. annuum and C. chinense . On the other hand, C. baccatum accumulates more Athila/Tat sequences. The FISH results show retrotransposons differentially scattered along chromosomes, with the exception of CRM family sequences, which mainly have a proximal accumulation associated with heterochromatin bands. Conclusions: The results confirm a close genomic relationship between C. annuum and C. chinense in comparison to C. baccatum . Centromeric GC-rich bands appeared to be associated with the accumulation regions of CRM elements, whereas terminal and subterminal AT- and GC-rich bands do not correspond to the accumulation of the retrotransposons in the three Capsicum species tested here.