Small RNA and Methylation Patterns Comparison in Common Bean (Phaseolus vulgaris L.) Genome

Phaseolus vulgaris is one of the most important legumes cultivated worldwide and plays an important role as a protein source especially in developing countries. The common bean genome was recently released for the Andean genotype G19833. Thus, we explored the genome structure at epigenetics level, based on small RNA patterns in parallel with transposons elements (TE) density and methylation patterns identified in the same genotype. It is well known that TEs expression are suppressed or silenced by small RNAs (sRNAs), and this could be at transcriptional (mostly 24nt sRNAs) or post-transcriptional level (mostly 21nt sRNAs). We did a comparison between G19833 and BAT93 sRNAs sequences, which are two genotypes from Andean and Mesoamerican gene pools, respectively, identifying the regions with high 24nt sRNAs pattern vs 21nt sRNAs pattern, and this in turn was contrasted with methylation levels and TEs density over the genome. Furthermore, those patterns were contrasted with recombination rate, gene density and genes locally duplicated. We could observe how the distribution of the methylation, TEs and sRNAs are positively correlated in the pericentromere regions, while the gene density and genes locally duplicated showed a negative correlation with all of them, showing high levels in the euchromatin regions. We could also see how the recombination rate is suppressed on the same regions where the TEs, methylation and small RNAs are increased.