Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.

The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), on...

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Autores principales: Ilaria Milano, Massimiliano Babbucci, Frank Panitz, Rob Ogden, Rasmus O Nielsen, Martin I Taylor, Sarah J Helyar, Gary R Carvalho, Montserrat Espiñeira, Miroslava Atanassova, Fausto Tinti, Gregory E Maes, Tomaso Patarnello, FishPopTrace Consortium, Luca Bargelloni
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Publicado: Public Library of Science (PLoS) 2011
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spelling oai:doaj.org-article:12846467067e401882bfe1fadcb872f02021-11-18T07:33:43ZNovel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.1932-620310.1371/journal.pone.0028008https://doaj.org/article/12846467067e401882bfe1fadcb872f02011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22132191/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), one of the most important demersal resources of European fisheries. Two sequencing platforms, the Roche 454 FLX (454) and the Illumina Genome Analyzer (GAII), were used for Single Nucleotide Polymorphisms (SNPs) discovery in the hake muscle transcriptome. De novo transcriptome assembly into unique contigs, annotation, and in silico SNP detection were carried out in parallel for 454 and GAII sequence data. High-throughput genotyping using the Illumina GoldenGate assay was performed for validating 1,536 putative SNPs. Validation results were analysed to compare the performances of 454 and GAII methods and to evaluate the role of several variables (e.g. sequencing depth, intron-exon structure, sequence quality and annotation). Despite well-known differences in sequence length and throughput, the two approaches showed similar assay conversion rates (approximately 43%) and percentages of polymorphic loci (67.5% and 63.3% for GAII and 454, respectively). Both NGS platforms therefore demonstrated to be suitable for large scale identification of SNPs in transcribed regions of non-model species, although the lack of a reference genome profoundly affects the genotyping success rate. The overall efficiency, however, can be improved using strict quality and filtering criteria for SNP selection (sequence quality, intron-exon structure, target region score).Ilaria MilanoMassimiliano BabbucciFrank PanitzRob OgdenRasmus O NielsenMartin I TaylorSarah J HelyarGary R CarvalhoMontserrat EspiñeiraMiroslava AtanassovaFausto TintiGregory E MaesTomaso PatarnelloFishPopTrace ConsortiumLuca BargelloniPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 11, p e28008 (2011)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Ilaria Milano
Massimiliano Babbucci
Frank Panitz
Rob Ogden
Rasmus O Nielsen
Martin I Taylor
Sarah J Helyar
Gary R Carvalho
Montserrat Espiñeira
Miroslava Atanassova
Fausto Tinti
Gregory E Maes
Tomaso Patarnello
FishPopTrace Consortium
Luca Bargelloni
Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.
description The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), one of the most important demersal resources of European fisheries. Two sequencing platforms, the Roche 454 FLX (454) and the Illumina Genome Analyzer (GAII), were used for Single Nucleotide Polymorphisms (SNPs) discovery in the hake muscle transcriptome. De novo transcriptome assembly into unique contigs, annotation, and in silico SNP detection were carried out in parallel for 454 and GAII sequence data. High-throughput genotyping using the Illumina GoldenGate assay was performed for validating 1,536 putative SNPs. Validation results were analysed to compare the performances of 454 and GAII methods and to evaluate the role of several variables (e.g. sequencing depth, intron-exon structure, sequence quality and annotation). Despite well-known differences in sequence length and throughput, the two approaches showed similar assay conversion rates (approximately 43%) and percentages of polymorphic loci (67.5% and 63.3% for GAII and 454, respectively). Both NGS platforms therefore demonstrated to be suitable for large scale identification of SNPs in transcribed regions of non-model species, although the lack of a reference genome profoundly affects the genotyping success rate. The overall efficiency, however, can be improved using strict quality and filtering criteria for SNP selection (sequence quality, intron-exon structure, target region score).
format article
author Ilaria Milano
Massimiliano Babbucci
Frank Panitz
Rob Ogden
Rasmus O Nielsen
Martin I Taylor
Sarah J Helyar
Gary R Carvalho
Montserrat Espiñeira
Miroslava Atanassova
Fausto Tinti
Gregory E Maes
Tomaso Patarnello
FishPopTrace Consortium
Luca Bargelloni
author_facet Ilaria Milano
Massimiliano Babbucci
Frank Panitz
Rob Ogden
Rasmus O Nielsen
Martin I Taylor
Sarah J Helyar
Gary R Carvalho
Montserrat Espiñeira
Miroslava Atanassova
Fausto Tinti
Gregory E Maes
Tomaso Patarnello
FishPopTrace Consortium
Luca Bargelloni
author_sort Ilaria Milano
title Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.
title_short Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.
title_full Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.
title_fullStr Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.
title_full_unstemmed Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.
title_sort novel tools for conservation genomics: comparing two high-throughput approaches for snp discovery in the transcriptome of the european hake.
publisher Public Library of Science (PLoS)
publishDate 2011
url https://doaj.org/article/12846467067e401882bfe1fadcb872f0
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