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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 were screened in three genomes of peppers (Solanaceae). The present study aimed to understand the genome relationships among  Capsicum annuum ,  C. chinense,  and  C. baccatum , based on a comparative analysis of the function, diversity and 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 were used to compare all repetitive fractions from a cytogenomic point of view.    Results  The qualification and quantification of LTR-retrotransposons (LTR-RT) families were contrasted with molecular cytogenetic data, and the results showed 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 lineage 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 showed retrotransposons differentially scattered along chromosomes, except for CRM lineage 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 may 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.

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