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

Milano, Ilaria, Babbucci, Massimiliano, Panitz, Frank, Ogden, Rob, Nielsen, Rasmus O., Taylor, Martin I. ORCID: https://orcid.org/0000-0002-3858-0712, Helyar, Sarah J., Carvalho, Gary R., Espiñeira, Montserrat, Atanassova, Miroslava, Tinti, Fausto, Maes, Gregory E., Patarnello, Tomaso and Bargelloni, Luca (2011) Novel tools for conservation genomics: Comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake. PLoS One, 6 (11). ISSN 1932-6203

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Abstract

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).

Item Type: Article
Additional Information: © 2011 Milano et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: Pure Connector
Date Deposited: 02 Dec 2013 13:44
Last Modified: 26 Sep 2022 05:37
URI: https://ueaeprints.uea.ac.uk/id/eprint/45072
DOI: 10.1371/journal.pone.0028008

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