Transposon insertions, 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 t...

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Authors: Sanseverino, Walter, Hénaff, Elizabeth, Vives, Cristina, Pinosio, Sara, Burgos-Paz, W., Morgante, Michele, Ramos-Onsins, Sebastian E., García-Mas, Jordi, Casacuberta, Josep M.
Format: article
Status:Published version
Publication Date:2015
Country:España
Institution:Consejo Superior de Investigaciones Científicas (CSIC)
Repository:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/250716
Online Access:http://hdl.handle.net/10261/250716
Access Level:Open access
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spelling Transposon insertions, structural variations, and SNPs contribute to the evolution of the melon genomeSanseverino, WalterHénaff, ElizabethVives, CristinaPinosio, SaraBurgos-Paz, W.Morgante, MicheleRamos-Onsins, Sebastian E.García-Mas, JordiCasacuberta, Josep M.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.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.Peer reviewedOxford University PressMinisterio de Ciencia e Innovación (España)Ministerio de Economía y Competitividad (España)Fundación Genoma EspañaConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202120212015info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/250716reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/AGL2013-43244-Rinfo:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/AGL2013-41834-Rhttps://doi.org/10.1093/molbev/msv152Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2507162026-05-22T06:33:51Z
dc.title.none.fl_str_mv Transposon insertions, structural variations, and SNPs contribute to the evolution of the melon genome
title Transposon insertions, structural variations, and SNPs contribute to the evolution of the melon genome
spellingShingle Transposon insertions, structural variations, and SNPs contribute to the evolution of the melon genome
Sanseverino, Walter
title_short Transposon insertions, structural variations, and SNPs contribute to the evolution of the melon genome
title_full Transposon insertions, structural variations, and SNPs contribute to the evolution of the melon genome
title_fullStr Transposon insertions, structural variations, and SNPs contribute to the evolution of the melon genome
title_full_unstemmed Transposon insertions, structural variations, and SNPs contribute to the evolution of the melon genome
title_sort Transposon insertions, structural variations, and SNPs contribute to the evolution of the melon genome
dc.creator.none.fl_str_mv Sanseverino, Walter
Hénaff, Elizabeth
Vives, Cristina
Pinosio, Sara
Burgos-Paz, W.
Morgante, Michele
Ramos-Onsins, Sebastian E.
García-Mas, Jordi
Casacuberta, Josep M.
author Sanseverino, Walter
author_facet Sanseverino, Walter
Hénaff, Elizabeth
Vives, Cristina
Pinosio, Sara
Burgos-Paz, W.
Morgante, Michele
Ramos-Onsins, Sebastian E.
García-Mas, Jordi
Casacuberta, Josep M.
author_role author
author2 Hénaff, Elizabeth
Vives, Cristina
Pinosio, Sara
Burgos-Paz, W.
Morgante, Michele
Ramos-Onsins, Sebastian E.
García-Mas, Jordi
Casacuberta, Josep M.
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Ciencia e Innovación (España)
Ministerio de Economía y Competitividad (España)
Fundación Genoma España
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
description 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.
publishDate 2015
dc.date.none.fl_str_mv 2015
2021
2021
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/250716
url http://hdl.handle.net/10261/250716
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/AGL2013-43244-R
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/AGL2013-41834-R
https://doi.org/10.1093/molbev/msv152
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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