Deciphering the repetitive DNA landscape in Phaseolus beans and Allied genera (Cajanus and Vigna) by a comparative cytogenomic approach

Abstract

Several bean species (Fabaceae) have been undergoing intensive genomic research, which includes the generation of massive amount of DNA sequence data. We performed a comparative investigation of the repetitive DNA composition in some bean species (Phaseolus vulgaris - Pvu, P. acutifolius - Pac, P. coccineus - Pco, Cajanus cajan - Cca, Vigna angularis - Van and V. nakashimae - Vna). Genomic sequences were obtained from the NCBI public database Cca/SRX031567, Pac/SRX1182015), Pco/SRX1182014, Pvu-andean accession/SRX1182008 and mesoamerican accession/SRX1182013, Vna/SRX758247 and Van/SRX7575509) and run in the Repeat Explorer pipeline using an all-to-all comparison analysis. Physical mapping of the most abundant repetitive elements was performed by FISH using mitotic chromosomes. Overall, the repetitive DNA fraction makes up around 30% of the genomes, except for both Vigna species (9.7% and 14.6%, for Van and Vna, respectively). LTR-retrotransposons represented the major class, with Ogre-Tat elements showing a large variation, followed by LTR-Chromovirus, satellite DNA repeats, LINEs and DNA transposons. The composition of satellite repeats was variable and four new families were identified, together with five previously described. All satellites were genus- or species-specific. Chromosomal mapping of LTR sequences (Chromovirus and Ogre) showed a differential accumulation on the pericentromeres of most chromosomes, particularly on Phaseolus. Among the satellite repeats, five were used for FISH (four newly identified). The three satellite families from Phaseolus showed different species-specific distribution. PacSAT363 was detected in 12 pericentromeres. PcoSAT36 and PcoSAT336 were accumulated at pericentromes, but PcoSAT336 were also located in some chromosome termini co-localized with 45 rDNA, suggesting that this satellite have probably originated from ribosomal sequences. Cajanus cajan and Vigna showed only one satellite repeat each. CcaSAT100 was located in 18 centromeres, while VanSAT174 corresponded to the 45 rDNA in Vna, but appeared also as an independent centromeric satellite repeat in Van. Our analysis indicates a very dynamic landscape on the evolution of repetitive DNA among beans. Retrotransposons appeared as the main component of genomes and showed higher accumulation in the pericentromeric heterochromatin of Phaseolus species. Satellite repeats were mostly centromeric or pericentromeric and frequently species-specific, suggesting a fast evolution of this type of sequence in the bean genomes.