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

Walter Sanseverino, Elizabeth Henaff, Cristina Vives, Sara Pinosio, William Burgos-Paz, Michele Morgante, Sebastián E. Ramos-Onsins, Jordi Garcia-Mas, Josep Maria Casacuberta

Research output: Contribution to journalArticle

Abstract

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 (SV) 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, SV, and transposon insertion polymorphisms. The variability found among seven 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 nonuniformly 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.

Original languageEnglish (US)
Pages (from-to)2760-2774
Number of pages15
JournalMolecular Biology and Evolution
Volume32
Issue number10
DOIs
Publication statusPublished - Jan 1 2015

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Keywords

  • evolution
  • melon
  • SNP
  • structural variation
  • transposon polymorphism

ASJC Scopus subject areas

  • Medicine(all)
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Sanseverino, W., Henaff, E., Vives, C., Pinosio, S., Burgos-Paz, W., Morgante, M., ... Casacuberta, J. M. (2015). Transposon insertions, structural variations, and SNPs contribute to the evolution of the melon genome. Molecular Biology and Evolution, 32(10), 2760-2774. https://doi.org/10.1093/molbev/msv152