Insights from Hi-C data regarding the Pacific salmon louse (Lepeophtheirus salmonis) sex chromosomes.
Salmon lice, Lepeophtheirus salmonis (family Caligidae), are ectoparasites that have negatively impacted the salmon aquaculture industry and vulnerable wild salmon populations. Researchers have studied salmon lice to better understand their biology to develop effective control strategies. In this st...
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Online Access: | https://doi.org/10.1093/g3journal/jkae087 https://pubmed.ncbi.nlm.nih.gov/38683737 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11228835/ |
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ftpubmed:38683737 2024-09-09T19:30:50+00:00 Insights from Hi-C data regarding the Pacific salmon louse (Lepeophtheirus salmonis) sex chromosomes. Flores, Anne-Marie Christensen, Kris A Siah, Ahmed Koop, Ben F 2024 Jul 08 https://doi.org/10.1093/g3journal/jkae087 https://pubmed.ncbi.nlm.nih.gov/38683737 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11228835/ eng eng Silverchair Information Systems https://doi.org/10.1093/g3journal/jkae087 https://pubmed.ncbi.nlm.nih.gov/38683737 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11228835/ © The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. G3 (Bethesda) ISSN:2160-1836 Volume:14 Issue:7 Pacific ZW sex determination farmed salmon ocean parasite sea lice Journal Article 2024 ftpubmed https://doi.org/10.1093/g3journal/jkae087 2024-07-10T16:02:00Z Salmon lice, Lepeophtheirus salmonis (family Caligidae), are ectoparasites that have negatively impacted the salmon aquaculture industry and vulnerable wild salmon populations. Researchers have studied salmon lice to better understand their biology to develop effective control strategies. In this study, we updated the chromosome-level reference genome assembly of the Pacific subspecies of L. salmonis using Hi-C data. The previous version placed contigs/scaffolds using an Atlantic salmon louse genetic map. By utilizing Hi-C data from Pacific salmon lice, we were able to properly assign locations to contigs/scaffolds previously unplaced or misplaced. This resulted in a more accurate genome assembly and a more comprehensive characterization of the sex chromosome unique to females (W). We found evidence that the same ZW-ZZ mechanism is common in both Atlantic and Pacific subspecies of salmon lice using PCR assays. The W chromosome was approximately 800 kb in size, which is ∼30 times smaller than the Z chromosome (24 Mb). The W chromosome contained 61 annotated genes, including 32 protein-coding genes, 27 long noncoding RNA (lncRNA) genes, and 2 pseudogenes. Among these 61 genes, 39 genes shared homology to genes found on other chromosomes, while 20 were unique to the W chromosome. Two genes of interest on the W chromosome, prohibitin-2 and kinase suppressor of ras-2, were previously identified as potential sex-linked markers in the salmon louse. However, we prioritized the 20 unique genes on the W chromosome as sex-determining candidates. This information furthers our understanding of the biology of this ectoparasite and may help in the development of more effective management strategies. Article in Journal/Newspaper Atlantic salmon PubMed Central (PMC) Pacific G3: Genes, Genomes, Genetics 14 7 |
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Open Polar |
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PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Pacific ZW sex determination farmed salmon ocean parasite sea lice |
spellingShingle |
Pacific ZW sex determination farmed salmon ocean parasite sea lice Flores, Anne-Marie Christensen, Kris A Siah, Ahmed Koop, Ben F Insights from Hi-C data regarding the Pacific salmon louse (Lepeophtheirus salmonis) sex chromosomes. |
topic_facet |
Pacific ZW sex determination farmed salmon ocean parasite sea lice |
description |
Salmon lice, Lepeophtheirus salmonis (family Caligidae), are ectoparasites that have negatively impacted the salmon aquaculture industry and vulnerable wild salmon populations. Researchers have studied salmon lice to better understand their biology to develop effective control strategies. In this study, we updated the chromosome-level reference genome assembly of the Pacific subspecies of L. salmonis using Hi-C data. The previous version placed contigs/scaffolds using an Atlantic salmon louse genetic map. By utilizing Hi-C data from Pacific salmon lice, we were able to properly assign locations to contigs/scaffolds previously unplaced or misplaced. This resulted in a more accurate genome assembly and a more comprehensive characterization of the sex chromosome unique to females (W). We found evidence that the same ZW-ZZ mechanism is common in both Atlantic and Pacific subspecies of salmon lice using PCR assays. The W chromosome was approximately 800 kb in size, which is ∼30 times smaller than the Z chromosome (24 Mb). The W chromosome contained 61 annotated genes, including 32 protein-coding genes, 27 long noncoding RNA (lncRNA) genes, and 2 pseudogenes. Among these 61 genes, 39 genes shared homology to genes found on other chromosomes, while 20 were unique to the W chromosome. Two genes of interest on the W chromosome, prohibitin-2 and kinase suppressor of ras-2, were previously identified as potential sex-linked markers in the salmon louse. However, we prioritized the 20 unique genes on the W chromosome as sex-determining candidates. This information furthers our understanding of the biology of this ectoparasite and may help in the development of more effective management strategies. |
format |
Article in Journal/Newspaper |
author |
Flores, Anne-Marie Christensen, Kris A Siah, Ahmed Koop, Ben F |
author_facet |
Flores, Anne-Marie Christensen, Kris A Siah, Ahmed Koop, Ben F |
author_sort |
Flores, Anne-Marie |
title |
Insights from Hi-C data regarding the Pacific salmon louse (Lepeophtheirus salmonis) sex chromosomes. |
title_short |
Insights from Hi-C data regarding the Pacific salmon louse (Lepeophtheirus salmonis) sex chromosomes. |
title_full |
Insights from Hi-C data regarding the Pacific salmon louse (Lepeophtheirus salmonis) sex chromosomes. |
title_fullStr |
Insights from Hi-C data regarding the Pacific salmon louse (Lepeophtheirus salmonis) sex chromosomes. |
title_full_unstemmed |
Insights from Hi-C data regarding the Pacific salmon louse (Lepeophtheirus salmonis) sex chromosomes. |
title_sort |
insights from hi-c data regarding the pacific salmon louse (lepeophtheirus salmonis) sex chromosomes. |
publisher |
Silverchair Information Systems |
publishDate |
2024 |
url |
https://doi.org/10.1093/g3journal/jkae087 https://pubmed.ncbi.nlm.nih.gov/38683737 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11228835/ |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
G3 (Bethesda) ISSN:2160-1836 Volume:14 Issue:7 |
op_relation |
https://doi.org/10.1093/g3journal/jkae087 https://pubmed.ncbi.nlm.nih.gov/38683737 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11228835/ |
op_rights |
© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. |
op_doi |
https://doi.org/10.1093/g3journal/jkae087 |
container_title |
G3: Genes, Genomes, Genetics |
container_volume |
14 |
container_issue |
7 |
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1809899810841427968 |