The salmon louse genome: Copepod features and parasitic adaptations

Skern‐Mauritzen, Rasmus; Malde, Ketil; Eichner, Christiane; Dondrup, Michael; Furmanek, Tomasz; Besnier, François; Komisarczuk, Anna Z.; Nuhn, Michael; Dalvin, Sussie; Edvardsen, Rolf B.; Klages, Sven; Huettel, Bruno; Stueber, Kurt; Grotmol, Sindre; Karlsbakk, Egil; Kersey, Paul J.; Leong, Jong S.; Glover, Kevin A.; Reinhardt, Richard; Lien, Sigbjørn; Jonassen, Inge; Koop, Ben F.; Nilsen, Frank

doi:10.1016/j.ygeno.2021.08.002

Cited by 21 publications

(51 citation statements)

References 138 publications

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“…Our results showed that salmon louse sex is determined based on a ZW sex-determining system which is in agreement with a recent analysis of the salmon louse genome [ 31 ]. Such a system has been suggested before based on one SNP in the prohibitin-2 gene [ 12 ] and on several SNPs in several other genes [ 13 ], among them the kinase suppressor of Ras 2.…”

Section: Discussionsupporting

confidence: 93%

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Sex differences in the early life stages of the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)

2022

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Salmon lice are ectoparasites on salmonids and feed on blood, mucus, and skin from their hosts. This causes high annual costs for treatment and control for the aquaculture industry. Salmon lice have a life cycle consisting of eight life stages. Sex determination by eye is only possible from the sixth stage onwards. A molecular sex determination has not been carried out so far, even though few individual sex-linked SNPs have been reported. In the present study, we used known sex-specific SNPs as a basis to sequence the complete sex-specific gene variants and used the sequence information to develop a sex determination assay. This assay could be used to determine the developmental speed of the two sexes already in the earliest life stages. Additionally, we sampled salmon lice in the nauplius II stage, determined the sex of each individual, pooled their RNA according to their sex, and used RNA sequencing to search for differences in gene expression and further sex-specific SNPs. We succeeded in developing a sex-determination assay that works on DNA or RNA from even the earliest larval stages of the salmon louse after hatching. At these early developmental stages, male salmon lice develop slightly quicker than females. We detected several previously unknown, sex-specific SNPs in our RNA-data seq, but only very few genes showed a differential expression between the sexes. Potential connections between SNPs, gene expression, and development are discussed.

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Section: Discussionsupporting

confidence: 93%

“…The correct mapping of the reads is thereby challenging. This calls for further improvements of the salmon lice genome [ 31 ], which was assembled based on reads with a length between 50 and 1100 base pairs [ 31 ]. New sequencing techniques allow for read lengths of more than 10 kb [ 52 ].…”

Section: Discussionmentioning

confidence: 99%

Sex differences in the early life stages of the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)

2022

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“…Male heterogamety, female heterogamety, haplodiploidy, and paternal genome elimination are examples of common sex determination systems (Blackmon et al, 2017 ). According to reports, the salmon lice genome is consistent with a female heterogamety containing both ZZ‐ZW and ZZ‐Z0 sex chromosomes (Danzmann et al, 2019 ; Skern‐Mauritzen et al, 2021 ). At the early stages of development, salmon lice lack distinguishable secondary sex features, therefore a sex‐specific marker is valuable for early sex identification.…”

Section: Introductionmentioning

confidence: 95%

IIb‐RAD‐sequencing coupled with random forest classification indicates regional population structuring and sex‐specific differentiation in salmon lice (Lepeophtheirus salmonis)

Guragain

Båtnes

Zobolas

et al. 2022

Ecology and Evolution

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The aquaculture industry has been dealing with salmon lice problems forming serious threats to salmonid farming. Several treatment approaches have been used to control the parasite. Treatment effectiveness must be optimized, and the systematic genetic differences between subpopulations must be studied to monitor louse species and enhance targeted control measures. We have used IIb‐RAD sequencing in tandem with a random forest classification algorithm to detect the regional genetic structure of the Norwegian salmon lice and identify important markers for sex differentiation of this species. We identified 19,428 single nucleotide polymorphisms (SNPs) from 95 individuals of salmon lice. These SNPs, however, were not able to distinguish the differential structure of lice populations. Using the random forest algorithm, we selected 91 SNPs important for geographical classification and 14 SNPs important for sex classification. The geographically important SNP data substantially improved the genetic understanding of the population structure and classified regional demographic clusters along the Norwegian coast. We also uncovered SNP markers that could help determine the sex of the salmon louse. A large portion of the SNPs identified to be under directional selection was also ranked highly important by random forest. According to our findings, there is a regional population structure of salmon lice associated with the geographical location along the Norwegian coastline.

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“…As the salmonid aquaculture has expanded to the extent that farmed salmonids outnumber wild salmonids by 2–3 orders of magnitude in some regions in the North Atlantic, the salmon lice populations have increased in parallel and currently inflict significant economic and ecological challenges 28 , 29 . The combined societal and ecological impacts of L. salmonis have spurred intense research and tool development, including modelling to assess ecological risk 30 , 31 , development of methodology for surveillance 25 , 32 , studies of population genetics 33 – 35 , resistance and resilience development against delousing agents 36 , 37 and molecular biology 38 – 41 . As a result, the salmon louse genome has been sequenced several times using various sequencing platforms, and independent genome assemblies have been made 41 , 42 —including two chromosome level assemblies.…”

Section: Introductionmentioning

confidence: 99%

“…The combined societal and ecological impacts of L. salmonis have spurred intense research and tool development, including modelling to assess ecological risk 30 , 31 , development of methodology for surveillance 25 , 32 , studies of population genetics 33 – 35 , resistance and resilience development against delousing agents 36 , 37 and molecular biology 38 – 41 . As a result, the salmon louse genome has been sequenced several times using various sequencing platforms, and independent genome assemblies have been made 41 , 42 —including two chromosome level assemblies.…”

Section: Introductionmentioning

confidence: 99%

The salmon louse genome may be much larger than sequencing suggests

Wyngaard

Skern‐Mauritzen

Malde

et al. 2022

Sci Rep

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The genome size of organisms impacts their evolution and biology and is often assumed to be characteristic of a species. Here we present the first published estimates of genome size of the ecologically and economically important ectoparasite, Lepeophtheirus salmonis (Copepoda, Caligidae). Four independent L. salmonis genome assemblies of the North Atlantic subspecies Lepeophtheirus salmonis salmonis, including two chromosome level assemblies, yield assemblies ranging from 665 to 790 Mbps. These genome assemblies are congruent in their findings, and appear very complete with Benchmarking Universal Single-Copy Orthologs analyses finding > 92% of expected genes and transcriptome datasets routinely mapping > 90% of reads. However, two cytometric techniques, flow cytometry and Feulgen image analysis densitometry, yield measurements of 1.3–1.6 Gb in the haploid genome. Interestingly, earlier cytometric measurements reported genome sizes of 939 and 567 Mbps in L. salmonis salmonis samples from Bay of Fundy and Norway, respectively. Available data thus suggest that the genome sizes of salmon lice are variable. Current understanding of eukaryotic genome dynamics suggests that the most likely explanation for such variability involves repetitive DNA, which for L. salmonis makes up ≈ 60% of the genome assemblies.

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The salmon louse genome: Copepod features and parasitic adaptations

Cited by 21 publications

References 138 publications

Sex differences in the early life stages of the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)

Sex differences in the early life stages of the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)

IIb‐RAD‐sequencing coupled with random forest classification indicates regional population structuring and sex‐specific differentiation in salmon lice (Lepeophtheirus salmonis)

The salmon louse genome may be much larger than sequencing suggests

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