ArticlePloS one2011
Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Fine-scale population structure of the northern hard clam (Evolutionary applications · 2023Article
- EST-Microsatellite Types and Structural Scenarios in European Hake Fisheries.Animals : an open access journal from MDPI · 2022Article
- Genomic Approaches for Conservation Management in Australia under Climate Change.Life (Basel, Switzerland) · 2021Review
- Article
- A high-throughput SNP discovery strategy for RNA-seq data.BMC genomics · 2019Article
- Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus.Parasites & vectors · 2018Article
- Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success.BMC research notes · 2016Article
- Transcriptome Characterization and Functional Marker Development in Sorghum Sudanense.PloS one · 2016Article
- Population-level consequences of complementary sex determination in a solitary parasitoid.BMC evolutionary biology · 2015Article
- Characterization of 40 single nucleotide polymorphism (SNP) via Tm-shift assay in the mud crab (Scylla paramamosain).Molecular biology reports · 2014Article
- Transcriptome analysis of the mud crab (Scylla paramamosain) by 454 deep sequencing: assembly, annotation, and marker discovery.PloS one · 2014Article
- On the optimal trimming of high-throughput mRNA sequence data.Frontiers in genetics · 2014Article
- A comparison of next generation sequencing technologies for transcriptome assembly and utility for RNA-Seq in a non-model bird.PloS one · 2014Article
- Phylogeography of the California sheephead, Semicossyphus pulcher: the role of deep reefs as stepping stones and pathways to antitropicality.Ecology and evolution · 2013Article
- Investigating the genetics of Bti resistance using mRNA tag sequencing: application on laboratory strains and natural populations of the dengue vector Aedes aegypti.Evolutionary applications · 2013Article
- Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinus phylogeny.BMC genomics · 2013Article
- SNP discovery in European anchovy (Engraulis encrasicolus, L) by high-throughput transcriptome and genome sequencing.PloS one · 2013Article
- Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data.BMC genomics · 2012Article
- A transcriptome map of perennial ryegrass (Lolium perenne L.).BMC genomics · 2012Article
- Analysis of genome survey sequences and SSR marker development for Siamese Mud Carp, Henicorhynchus siamensis, using 454 pyrosequencing.International journal of molecular sciences · 2012Article
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15 authors.
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No grant is acknowledged in the PubMed record.
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).
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