Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis

Caligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. In this study, we report a chromosome-scale assembly of the sea louse (C. rogercresseyi) genome based on single-molecul...

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Autores principales: Gallardo-Escárate, Cristian, Valenzuela-Muñoz, Valentina, Nuñez-Acuña, Gustavo, Valenzuela-Miranda, Diego, Gonçalves, Ana Teresa, Escobar-Sepulveda, Hugo, Liachko, Ivan, Nelson, Bradley, Roberts, Steven, Warren, Wesley
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Data Descriptor
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7878743/
https://www.ncbi.nlm.nih.gov/pubmed/33574331
http://dx.doi.org/10.1038/s41597-021-00842-w
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author Gallardo-Escárate, Cristian
Valenzuela-Muñoz, Valentina
Nuñez-Acuña, Gustavo
Valenzuela-Miranda, Diego
Gonçalves, Ana Teresa
Escobar-Sepulveda, Hugo
Liachko, Ivan
Nelson, Bradley
Roberts, Steven
Warren, Wesley
author_facet Gallardo-Escárate, Cristian
Valenzuela-Muñoz, Valentina
Nuñez-Acuña, Gustavo
Valenzuela-Miranda, Diego
Gonçalves, Ana Teresa
Escobar-Sepulveda, Hugo
Liachko, Ivan
Nelson, Bradley
Roberts, Steven
Warren, Wesley
author_sort Gallardo-Escárate, Cristian
collection PubMed
description Caligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. In this study, we report a chromosome-scale assembly of the sea louse (C. rogercresseyi) genome based on single-molecule real-time sequencing (SMRT) and proximity ligation (Hi-C) analysis. Coding RNAs and non-coding RNAs, and specifically long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were identified through whole transcriptome sequencing from different life stages. A total of 23,686 protein-coding genes and 12,558 non-coding RNAs were annotated. In addition, 6,308 lncRNAs and 5,774 miRNAs were found to be transcriptionally active from larvae to adult stages. Taken together, this genomic resource for C. rogercresseyi represents a valuable tool to develop sustainable control strategies in the salmon aquaculture industry.
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spelling pubmed-78787432021-02-24 Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis Gallardo-Escárate, Cristian Valenzuela-Muñoz, Valentina Nuñez-Acuña, Gustavo Valenzuela-Miranda, Diego Gonçalves, Ana Teresa Escobar-Sepulveda, Hugo Liachko, Ivan Nelson, Bradley Roberts, Steven Warren, Wesley Sci Data Data Descriptor Caligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. In this study, we report a chromosome-scale assembly of the sea louse (C. rogercresseyi) genome based on single-molecule real-time sequencing (SMRT) and proximity ligation (Hi-C) analysis. Coding RNAs and non-coding RNAs, and specifically long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were identified through whole transcriptome sequencing from different life stages. A total of 23,686 protein-coding genes and 12,558 non-coding RNAs were annotated. In addition, 6,308 lncRNAs and 5,774 miRNAs were found to be transcriptionally active from larvae to adult stages. Taken together, this genomic resource for C. rogercresseyi represents a valuable tool to develop sustainable control strategies in the salmon aquaculture industry. Nature Publishing Group UK 2021-02-11 /pmc/articles/PMC7878743/ /pubmed/33574331 http://dx.doi.org/10.1038/s41597-021-00842-w Text en © The Author(s) 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files associated with this article.
spellingShingle Data Descriptor
Gallardo-Escárate, Cristian
Valenzuela-Muñoz, Valentina
Nuñez-Acuña, Gustavo
Valenzuela-Miranda, Diego
Gonçalves, Ana Teresa
Escobar-Sepulveda, Hugo
Liachko, Ivan
Nelson, Bradley
Roberts, Steven
Warren, Wesley
Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis
title Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis
title_full Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis
title_fullStr Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis
title_full_unstemmed Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis
title_short Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis
title_sort chromosome-scale genome assembly of the sea louse caligus rogercresseyi by smrt sequencing and hi-c analysis
topic Data Descriptor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7878743/
https://www.ncbi.nlm.nih.gov/pubmed/33574331
http://dx.doi.org/10.1038/s41597-021-00842-w
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