Virginia Institute of Marine Science
The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing(RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. without reference genomes.Here, the performances of two building-loci pipelines, STACKS 2 and Meyer’s 2b-RAD v2.1 pipeline, were compared using a diverse set of aquatic species representing different genomic and/or population structure scenarios. Two bivalve species (Manila clam and common edible cockle) and three fish species (brown trout, silver catfish and small-spotted catshark) were studied. Four SNP panels were evaluated in each species to test both different building-loci pipelines and criteria for SNP selection. Furthermore, for Manila clam and brown trout, a reference genome approach was used as control.
STACKS 2, 2b-RAD v2.1 pipeline, de novo approach, Bowtie 1, Reference genome approach, Bivalves, Fish, Population genomics
Casanova, Adrian; Maroso, Francesco; (...); Verissimo, Ana; and et al, Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species (2021). BMC Genomics, 22(150), 1-16.