Transposon insertion, structural variations and SNPs contribute to the evolution of the melon genome

The availability of extensive databases of crop genome sequences should allow analysis of crop variability at an unprecedented scale, which should have an important impact in plant breeding. However, up to now the analysis of genetic variability at the whole-genome scale has been mainly restricted to single nucleotide polymorphisms (SNPs). This is a strong limitation as structural variation and transposon insertion polymorphisms are frequent in plant species and have had an important mutational role in crop domestication and breeding. Here we present the first comprehensive analysis of melon genetic diversity, which includes a detailed analysis of SNPs, structural variation and transposon insertion polymorphisms.The variability found among 7 melon varieties representing the species diversity and including wild accessions and highly-breed lines, is relatively high due in part to the marked divergence of some lineages. The diversity is distributed non-uniformly across the genome, being lower at the extremes of the chromosomes and higher in the pericentromeric regions, which is compatible with the effect of purifying selection and recombination forces over functional regions. Additionally, this variability is greatly reduced among elite varieties, probably due to selection during breeding. We have found some chromosomal regions showing a high differentiation of the elite varieties versus the rest, which could be considered as strongly-selected candidate regions. Our data also suggest that transposons and SV may be at the origin of an important fraction of the variability in melon, which highlights the importance of analyzing all types of genetic variability to understand crop genome evolution.