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Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish

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Published on: October 27, 2017

SNP discovery using Next Generation Transcriptomic Sequencing in Atlantic herring (Clupea harengus).

Sarah J Helyar¹, Morten T Limborg, Dorte Bekkevold

¹Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom. sarah.helyar@matis.is

|August 11, 2012

Summary

Researchers developed 578 Single Nucleotide Polymorphisms (SNPs) for Atlantic herring using Next Generation Sequencing (NGS). This cost-effective method provides valuable genomic resources for population genetics and fisheries management.

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Area of Science:

Population genetics
Genomics
Evolutionary biology

Background:

Genomic resources for Atlantic herring (Clupea harengus) are limited.
Next Generation Sequencing (NGS) has advanced population genetics for non-model species.
Single Nucleotide Polymorphisms (SNPs) offer cost-effective high-throughput genotyping.

Purpose of the Study:

To develop a panel of 578 SNPs for Atlantic herring.
To establish genomic resources for population discrimination and genomic studies.
To maximize cost and time efficiencies in SNP development.

Main Methods:

Combined NGS (454 GS FLX) and high-throughput genotyping (Illumina GoldenGate assay).
De novo sequence clustering, contig assembly, and read mapping for SNP discovery.
In silico selection of candidate SNPs to minimize ascertainment bias and laboratory validation.

Main Results:

Successfully developed 578 SNPs for Atlantic herring.
The in silico approach reduced ascertainment bias, enabling genotyping of SNPs with a wider range of minor allele frequencies (MAFs).
The developed genomic resources are suitable for population discrimination and genomic studies.

Conclusions:

The developed SNP panel is a valuable resource for Atlantic herring research.
The combined NGS and in silico approach offers an efficient method for SNP development in non-model organisms.
These genomic resources will support population genomic studies and fisheries management.