Utility of 18S rDNA and ITS sequences as population markers for Lepeophtheirus salmonis (Copepoda: Caligidae) parasitising Atlantic salmon (Salmo salar) in Scotland

Abstract

Genetic differentiation within the salmon louse Lepeophtheirus salmonis (Krøyer, 1837), was investigated by the sequencing of specific nucleotide regions. Partial sequences of the 18S ribosomal RNA gene and the ribosomal internal transcribed spacer (ITS-1) region from single sea lice were amplified by the polymerase chain reaction (PCR). Lice were collected from wild and farmed Atlantic salmon (Salmo salar L., 1758) from nine selected localities around the Scottish coastline. A 0.9kb fragment of the 18S ribosomal RNA gene was amplified and compared for several samples of lice which showed no observable differences between the lice from different collection sites confirming the absence of cryptic species. The 454 nucleotide ITS-1 sequence showed differences between derived sequences from 13 sea lice samples from 4 collection sites which included 2 farm sites and 2 sites where lice were taken from wild fish. Across all samples, there was a 92.14% similarity in the ITS-1 sequence. The percentage similarity in the ITS-1 sequence in samples office from two fish farms were 99.71% (site A) and 95.72% (site D) but only 86.90% (site B) and 86.03% (site C) similarity was shown in lice samples taken from sites where wild salmonids were caught. The greater similarity between the ITS-1 sequence within farm sites may be attributed to a restricted gene flow within lice populations in Atlantic salmon cage sites.

Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact

“…The compared sequences contained both relatively evolutionarily conserved (fragments of 18S and 28S rDNA and the complete 5.8S rDNA) and evolutionary variable genomic regions (ITS1 and ITS2). For different taxa, the ITS1 and ITS2 sequences vary significantly among individuals at the inter- and intrapopulation levels; furthermore, these sequences can exhibit intragenomic variability [ 25 , 41 , 53 , 54 ]. Recently, a high level of intrapopulation polymorphism of the 28S rDNA sequences was observed within Oithona spp.…”

Geographic and temporal genetic structure in Lepeophtheirus salmonis from four salmon farms along the northwest and west coasts of Ireland: results from a microsatellite analysis

“…The varying degree of differentiation evident from RAPD analyses is potentially an artefact of insensitivity to detect small changes in the L. salmonis populations under study and difficulties in reproducibility. Shinn et al (2000) used L. salmonis from nine localities around the Scottish coastline from both farmed and wild salmonid hosts, and found greater similarity of L. salmonis ITS-1 sequences within farms than for the wild population sources.…”

Caligus elongatus Nordmann genotypes on wild and farmed fish

“…For the salmon louse, L. salmonis , a close relative of C. elongatus , nucleotide sequence (Shinn, Banks, Tange, Bron, Sommerville, Aoki & Wootten 2000; Tjensvoll, Glover & Nylund 2006) and microsatellite (Nolan, Martin, Kelly, Glennon, Palmer, Smith, McCormack & Powell 2000; Todd, Walker, Ritchie, Graves & Walker 2004) analyses have demonstrated that the Atlantic salmon lice comprise a large population with no apparent clusters based on geographical locality. High dispersal of the parasites between geographically distant salmon louse populations causes a considerable genetic exchange and limits the divergence into distinct genetic variants.…”