PRJNA447894
Lepeophtheirus salmonis resequencing for genomic variation and 200K SNP chip design.
Lepeophtheirus salmonis, commonly know as the salmon louse or sea louse, is an ectoparasitic copepod of both Pacific and Atlantic salmon species. In this work we sought to characterise genomic variation in both the Atlantic and Pacific subspecies of L. salmonis by whole-genome Illumina-based re-sequencing with the aim of identifying SNPs suitable for development of a 200K SNP chip. Heterozygosity in these samples was high, particularly in the Pacific subspecies, where a kmer-based analysis suggested a polymorphism rate of up to 1/46 bp (median rate 1/72 bp) in an individual louse. The Atlantic subspecies in contrast demonstrated a median rate of 1/173 bp for the individuals analysed. SNPs identified from this re-sequencing data were used to generate a 200K SNP chip with cross-compatibility in both Atlantic and Pacific subspecies. This SNP chip is being used to generate a high-density linkage map (Danzmann et al) and to analyse genomic signals associated with reduced efficacy of a delousing drug in the Pacific (Messmer et al).