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De novo assembly and functional annotation of the nervous system transcriptome in the Caribbean spiny lobster <i>Panulirus argus</i>
Indexado
WoS WOS:000742790700001
Scopus SCOPUS_ID:85123086917
DOI 10.1007/S00338-021-02213-8
Año 2022
Tipo artículo de investigación

Citas Totales

Autores Afiliación Chile

Instituciones Chile

% Participación
Internacional

Autores
Afiliación Extranjera

Instituciones
Extranjeras


Abstract



The spiny lobster Panulirus argus is an ecologically relevant species in shallow water coral reefs and the target of the most lucrative fishery in the greater Caribbean region. This study reports, for the first time, the nervous system transcriptome of the Caribbean spiny lobster Panulirus argus assembled from short Illumina 150 bp PE raw reads. A total of 60,213,359 pairs of raw reads were assembled using the Elvers pipeline. The assembly resulted in a total of 206,273 transcripts with N50 of 1341 bp and L50 of 23,665 contigs. Analysis of this filtered assembly by BUSCO resulted in the identification of 92.49% universal orthologs. Analysis of core GFs completeness with the Arthropoda database resulted in the identification of 77.8% of 1936 Core GFs. Functional gene annotation was conducted using the web server TRAPID and the dammit pipeline. TRAPID and dammit provided functional annotation for 25,617 and 57,984 of transcripts, respectively. Lastly, gene enrichment analyses were conducted using the Gene ontology (GO) and KEGG pathway analyses (Kaas) databases. This transcriptome represents the first step to improving the understanding of the molecular underpinnings of viral infection and behavioral immunity (i.e., social distancing) in this iconic coral reef-associated invertebrate. The development of this and other genomic resources is of utmost importance as they will improve the understanding of the biology of P. argus while also aiding in fishery management and conservation strategies of this iconic coral reef-dwelling, heavily fished marine invertebrate.

Revista



Revista ISSN
Coral Reefs 0722-4028

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Disciplinas de Investigación



WOS
Marine & Freshwater Biology
Scopus
Sin Disciplinas
SciELO
Sin Disciplinas

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Publicaciones WoS (Ediciones: ISSHP, ISTP, AHCI, SSCI, SCI), Scopus, SciELO Chile.

Colaboración Institucional



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Autores - Afiliación



Ord. Autor Género Institución - País
1 BAEZA-MIGUELES, JUAN ANTONIO Hombre Clemson Univ - Estados Unidos
Smithsonian Marine Stn Ft Pierce - Estados Unidos
Universidad Católica del Norte - Chile
Clemson University - Estados Unidos
Smithsonian Marine Station - Estados Unidos
2 Veldsman, Werner Pieter Hombre Chinese Univ Hong Kong - China
Univ Lausanneand - Suiza
Chinese University of Hong Kong - Hong Kong
Swiss Institute of Bioinformatics - Suiza
SIB Swiss Institute of Bioinformatics - Suiza
3 Chu, Ka Hou - Chinese Univ Hong Kong - China
Southern Marine Sci & Engn Guangdong Lab Guangzho - China
Hong Kong Univ Sci & Technol - China
Chinese University of Hong Kong - Hong Kong
Hong Kong University of Science and Technology - Hong Kong
Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) - Hong Kong

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Financiamiento



Fuente
Research Grants Council, University Grants Committee
Collaborative Research Fund
Research Grants Council, Hong Kong Special Administrative Region, China

Muestra la fuente de financiamiento declarada en la publicación.

Agradecimientos



Agradecimiento
JAB thanks Dr. Vincent P. Richards for bioinformatics support during the development of this project. The comments of two anonymous referees permitted us to improve earlier versions of this manuscript. The work presented in this paper was partially supported by a grant from the Collaborative Research Fund (project no. C4042-14G), Research Grants Council, Hong Kong Special Administrative Region, China.
JAB thanks Dr. Vincent P. Richards for bioinformatics support during the development of this project. The comments of two anonymous referees permitted us to improve earlier versions of this manuscript. The work presented in this paper was partially supported by a grant from the Collaborative Research Fund (project no. C4042-14G), Research Grants Council, Hong Kong Special Administrative Region, China.

Muestra la fuente de financiamiento declarada en la publicación.