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Transposon insertions, structural variations, and SNPs contribute to the evolution of the melon genome
- Source :
- Molecular biology and evolution 32 (2015): 2760–2774. doi:10.1093/molbev/msv152, info:cnr-pdr/source/autori:Sanseverino, Walter; Henaff, Elizabeth; Vives, Cristina; Pinosio, Sara; Burgos-Paz, William; Morgante, Michele; Ramos-Onsins, Sebastian E.; Garcia-Mas, Jordi; Casacuberta, Josep Maria/titolo:Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome/doi:10.1093%2Fmolbev%2Fmsv152/rivista:Molecular biology and evolution/anno:2015/pagina_da:2760/pagina_a:2774/intervallo_pagine:2760–2774/volume:32, Dipòsit Digital de Documents de la UAB, Universitat Autònoma de Barcelona, Digital.CSIC. Repositorio Institucional del CSIC, instname
- Publication Year :
- 2015
- Publisher :
- Oxford University Press, 2015.
-
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.<br />This work was supported by Ministerio de Ciencia e Innovación (grant BFU2009-11932 to J.M.C. and grant AGL2012-40130-C02-01 to J.G.-M.); Ministerio de Economía y Competitividad (grant AGL2013-43244-R to J.M.C., grant AGL2013-41834-R to S.E.R.-O., and grant AGL2009-12698-C02-01 to J.G.-M.); and Fundación Genoma España to J.G.-M.
- Subjects :
- transposon polymorphism
Genome evolution
Evolution
SNP
Single-nucleotide polymorphism
Biology
Polymorphism, Single Nucleotide
Genetic analysis
Genome
Evolution, Molecular
Structural variation
Transposon polymorphism
evolution
Genetic variation
melon
Genetics
Genetic variability
Selection, Genetic
Molecular Biology
Phylogeny
Ecology, Evolution, Behavior and Systematics
Genetic diversity
Nucleotides
structural variation
food and beverages
Melon
Cucurbitaceae
Mutagenesis, Insertional
Genetic Loci
DNA Transposable Elements
Cucumis sativus
Gene Deletion
Genome, Plant
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Molecular biology and evolution 32 (2015): 2760–2774. doi:10.1093/molbev/msv152, info:cnr-pdr/source/autori:Sanseverino, Walter; Henaff, Elizabeth; Vives, Cristina; Pinosio, Sara; Burgos-Paz, William; Morgante, Michele; Ramos-Onsins, Sebastian E.; Garcia-Mas, Jordi; Casacuberta, Josep Maria/titolo:Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome/doi:10.1093%2Fmolbev%2Fmsv152/rivista:Molecular biology and evolution/anno:2015/pagina_da:2760/pagina_a:2774/intervallo_pagine:2760–2774/volume:32, Dipòsit Digital de Documents de la UAB, Universitat Autònoma de Barcelona, Digital.CSIC. Repositorio Institucional del CSIC, instname
- Accession number :
- edsair.doi.dedup.....2568d0f3469df3588365e639792c3ae3
- Full Text :
- https://doi.org/10.1093/molbev/msv152