ITEM METADATA RECORD
Title: Novel Tools for Conservation Genomics: Comparing Two High-Throughput Approaches for SNP Discovery in the Transcriptome of the European Hake
Authors: Milano, Ilaria ×
Babbucci, Massimiliano
Panitz, Frank
Ogden, Rob
Nielsen, Rasmus O
Taylor, Martin I
Helyar, Sarah J
Carvalho, Gary R
Espineira, Montserrat
Atanassova, Miroslava
Tinti, Fausto
Maes, Gregory E
Patarnello, Tomaso
Bargelloni, Luca #
Issue Date: Nov-2011
Publisher: Public Library of Sciene
Series Title: PLoS One vol:6 issue:11 pages:-
Article number: e28008
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).
ISSN: 1932-6203
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Laboratory for Animal Biodiversity and Systematics (-)
× corresponding author
# (joint) last author

Files in This Item:

There are no files associated with this item.

 


All items in Lirias are protected by copyright, with all rights reserved.

© Web of science