Título

De Novo assembly and annotation of the Pacific calico scallop (Argopecten ventricosus) transcriptome for immune-related gene discovery

Autor

RUTH ESCAMILLA MONTES

GENARO DIARTE PLATA

GABRIELA BERENICE MENDOZA MALDONADO

Aarón Barraza Celis

Carlos Eliud Angulo Valadez

Seyed Hossein Hoseinifar

Jesús Arturo Fierro Coronado

ANTONIO LUNA GONZALEZ

Nivel de Acceso

Acceso Abierto

Licencia

http://creativecommons.org/licenses/by-nc-nd/4.0

Referencia de publicación

doi: DOI: 10.3856/vol50-issue2-fulltext-2705

URL/URL: https://www.lajar.cl/index.php/rlajar/article/view/vol50-issue2-fulltext-2705

ISSN/ISSN: 0718560X

Materias

Argopecten ventricosus, calico scallop, transcriptome, bivalve, immune genes - (AUTOR) BIOLOGÍA Y QUÍMICA - (CTI) CIENCIAS DE LA VIDA - (CTI) BIOLOGÍA ANIMAL (ZOOLOGÍA) - (CTI) INMUNOLOGÍA - (CTI) INMUNOLOGÍA - (CTI)

Resumen o descripción

"Invertebrates' immune defense mechanisms play a critical role in pathogen recognition and elimination. De novo assembly and annotation of the Argopecten ventricosus transcriptome were performed for the immune-related gene identification. Scallops (height: 4.4 cm) were challenged with inactivated Vibrio parahaemolyticus IPNGS16. The RNA from different tissues was pooled for a single cDNA library construction sequenced by NextSeq 500 platform 2×75 paired‐end chemistry. Before de novo assembling with Trinity, reads were analyzed with FastQC, Trimmomatic, and Prinseq. Assembled sequences were analyzed by CD-HIT-EST and TransDecoder. The corresponding annotation was performed against NCBI-nr, RefSeq protein, and KAAS (KEGG) databases. The Trinity assembly yielded 107,516 contigs. TransDecoder yielded 25,285 sequences as CDSs of which, 16,123 were annotated against the NCBI-nr protein, most of them scored with Crassostrea gigas data. Gene ontology mapped sequences (15,262) were classified in molecular functions (~13,000), cellular components (~11,000), and biological processes (~13,000). The KAAS analysis showed biological categories for metabolism (13%), cellular processes (12%), genetic information processing (10%), organismal systems (19%), environmental information (13%), and human diseases (33 %). Within the organismal systems, 467 immune-related genes (KO) were identified. Sixty-four immune-related genes were annotated/blasted against the NCBI-nr and RefSeq protein databases. An RT-qPCR was performed to analyze the expression level of immune-related genes obtained in the transcriptome analysis in scallops (height 4.5 cm) treated with probiotic bacilli added to culture water. Bacilli significantly increased the expression of the HSP70 and PGRP genes. The gene transcripts analysis of A. ventricosus will better understand its immune response against pathogens in culture systems."

Editor

Pontificia Universidad Catolica de Valparaiso

Fecha de publicación

2022

Tipo de publicación

Artículo

Versión de la publicación

Versión publicada

Recurso de información

http://cibnor.repositorioinstitucional.mx/jspui/handle/1001/2828

Formato

application/pdf

Fuente

Latin American Journal of Aquatic Research

Idioma

Inglés

Sugerencia de citación

Escamilla-Montes R, Diarte-Plata G, Mendoza-Maldonado G, Barraza A, Angulo C, Hossein Hoseinifar S, Fierro-Coronado J, Luna-González A. De Novo assembly and annotation of the Pacific calico scallop (Argopecten ventricosus) transcriptome for immune-related gene discovery. Lat. Am. J. Aquat. Res.. 2022;50(2): 212-226. Available from: doi:10.3856/vol50-issue2-fulltext-2705

Repositorio Orígen

Repositorio Institucional CIBNOR

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