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Transcriptome sequencing for SNP discovery across Cucumis melo

BACKGROUND: Melon (Cucumis melo L.) is a highly diverse species that is cultivated worldwide. Recent advances in massively parallel sequencing have begun to allow the study of nucleotide diversity in this species. The Sanger method combined with medium-throughput 454 technology were used in a previo...

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Autores principales: Blanca, José, Esteras, Cristina, Ziarsolo, Pello, Pérez, Daniel, Fernández-Pedrosa, Victoria, Collado, Carmen, Rodríguez de Pablos, Raquel, Ballester, Alida, Roig, Cristina, Cañizares, Joaquín, Picó, Belén
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3473316/
https://www.ncbi.nlm.nih.gov/pubmed/22726804
http://dx.doi.org/10.1186/1471-2164-13-280
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author Blanca, José
Esteras, Cristina
Ziarsolo, Pello
Pérez, Daniel
Fernández-Pedrosa, Victoria
Collado, Carmen
Rodríguez de Pablos, Raquel
Ballester, Alida
Roig, Cristina
Cañizares, Joaquín
Picó, Belén
author_facet Blanca, José
Esteras, Cristina
Ziarsolo, Pello
Pérez, Daniel
Fernández-Pedrosa, Victoria
Collado, Carmen
Rodríguez de Pablos, Raquel
Ballester, Alida
Roig, Cristina
Cañizares, Joaquín
Picó, Belén
author_sort Blanca, José
collection PubMed
description BACKGROUND: Melon (Cucumis melo L.) is a highly diverse species that is cultivated worldwide. Recent advances in massively parallel sequencing have begun to allow the study of nucleotide diversity in this species. The Sanger method combined with medium-throughput 454 technology were used in a previous study to analyze the genetic diversity of germplasm representing 3 botanical varieties, yielding a collection of about 40,000 SNPs distributed in 14,000 unigenes. However, the usefulness of this resource is limited as the sequenced genotypes do not represent the whole diversity of the species, which is divided into two subspecies with many botanical varieties variable in plant, flowering, and fruit traits, as well as in stress response. As a first step to extensively document levels and patterns of nucleotide variability across the species, we used the high-throughput SOLiD™ system to resequence the transcriptomes of a set of 67 genotypes that had previously been selected from a core collection representing the extant variation of the entire species. RESULTS: The deep transcriptome resequencing of all of the genotypes, grouped into 8 pools (wild African agrestis, Asian agrestis and acidulus, exotic Far Eastern conomon, Indian momordica and Asian dudaim and flexuosus, commercial cantalupensis, subsp. melo Asian and European landraces, Spanish inodorus landraces, and Piel de Sapo breeding lines) yielded about 300 M reads. Short reads were mapped to the recently generated draft genome assembly of the DHL line Piel de Sapo (inodorus) x Songwhan Charmi (conomon) and to a new version of melon transcriptome. Regions with at least 6X coverage were used in SNV calling, generating a melon collection with 303,883 variants. These SNVs were dispersed across the entire C. melo genome, and distributed in 15,064 annotated genes. The number and variability of in silico SNVs differed considerably between pools. Our finding of higher genomic diversity in wild and exotic agrestis melons from India and Africa as compared to commercial cultivars, cultigens and landraces from Eastern Europe, Western Asia and the Mediterranean basin is consistent with the evolutionary history proposed for the species. Group-specific SNVs that will be useful in introgression programs were also detected. In a sample of 143 selected putative SNPs, we verified 93% of the polymorphisms in a panel of 78 genotypes. CONCLUSIONS: This study provides the first comprehensive resequencing data for wild, exotic, and cultivated (landraces and commercial) melon transcriptomes, yielding the largest melon SNP collection available to date and representing a notable sample of the species diversity. This data provides a valuable resource for creating a catalog of allelic variants of melon genes and it will aid in future in-depth studies of population genetics, marker-assisted breeding, and gene identification aimed at developing improved varieties.
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spelling pubmed-34733162012-10-18 Transcriptome sequencing for SNP discovery across Cucumis melo Blanca, José Esteras, Cristina Ziarsolo, Pello Pérez, Daniel Fernández-Pedrosa, Victoria Collado, Carmen Rodríguez de Pablos, Raquel Ballester, Alida Roig, Cristina Cañizares, Joaquín Picó, Belén BMC Genomics Research Article BACKGROUND: Melon (Cucumis melo L.) is a highly diverse species that is cultivated worldwide. Recent advances in massively parallel sequencing have begun to allow the study of nucleotide diversity in this species. The Sanger method combined with medium-throughput 454 technology were used in a previous study to analyze the genetic diversity of germplasm representing 3 botanical varieties, yielding a collection of about 40,000 SNPs distributed in 14,000 unigenes. However, the usefulness of this resource is limited as the sequenced genotypes do not represent the whole diversity of the species, which is divided into two subspecies with many botanical varieties variable in plant, flowering, and fruit traits, as well as in stress response. As a first step to extensively document levels and patterns of nucleotide variability across the species, we used the high-throughput SOLiD™ system to resequence the transcriptomes of a set of 67 genotypes that had previously been selected from a core collection representing the extant variation of the entire species. RESULTS: The deep transcriptome resequencing of all of the genotypes, grouped into 8 pools (wild African agrestis, Asian agrestis and acidulus, exotic Far Eastern conomon, Indian momordica and Asian dudaim and flexuosus, commercial cantalupensis, subsp. melo Asian and European landraces, Spanish inodorus landraces, and Piel de Sapo breeding lines) yielded about 300 M reads. Short reads were mapped to the recently generated draft genome assembly of the DHL line Piel de Sapo (inodorus) x Songwhan Charmi (conomon) and to a new version of melon transcriptome. Regions with at least 6X coverage were used in SNV calling, generating a melon collection with 303,883 variants. These SNVs were dispersed across the entire C. melo genome, and distributed in 15,064 annotated genes. The number and variability of in silico SNVs differed considerably between pools. Our finding of higher genomic diversity in wild and exotic agrestis melons from India and Africa as compared to commercial cultivars, cultigens and landraces from Eastern Europe, Western Asia and the Mediterranean basin is consistent with the evolutionary history proposed for the species. Group-specific SNVs that will be useful in introgression programs were also detected. In a sample of 143 selected putative SNPs, we verified 93% of the polymorphisms in a panel of 78 genotypes. CONCLUSIONS: This study provides the first comprehensive resequencing data for wild, exotic, and cultivated (landraces and commercial) melon transcriptomes, yielding the largest melon SNP collection available to date and representing a notable sample of the species diversity. This data provides a valuable resource for creating a catalog of allelic variants of melon genes and it will aid in future in-depth studies of population genetics, marker-assisted breeding, and gene identification aimed at developing improved varieties. BioMed Central 2012-06-24 /pmc/articles/PMC3473316/ /pubmed/22726804 http://dx.doi.org/10.1186/1471-2164-13-280 Text en Copyright ©2012 Blanca et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Blanca, José
Esteras, Cristina
Ziarsolo, Pello
Pérez, Daniel
Fernández-Pedrosa, Victoria
Collado, Carmen
Rodríguez de Pablos, Raquel
Ballester, Alida
Roig, Cristina
Cañizares, Joaquín
Picó, Belén
Transcriptome sequencing for SNP discovery across Cucumis melo
title Transcriptome sequencing for SNP discovery across Cucumis melo
title_full Transcriptome sequencing for SNP discovery across Cucumis melo
title_fullStr Transcriptome sequencing for SNP discovery across Cucumis melo
title_full_unstemmed Transcriptome sequencing for SNP discovery across Cucumis melo
title_short Transcriptome sequencing for SNP discovery across Cucumis melo
title_sort transcriptome sequencing for snp discovery across cucumis melo
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3473316/
https://www.ncbi.nlm.nih.gov/pubmed/22726804
http://dx.doi.org/10.1186/1471-2164-13-280
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