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Identification of immune-related SNPs in the transcriptome of Mytilus chilensis through high-throughput sequencing.
Fish Shellfish Immunol 2013; 35(6):1899-905FS

Abstract

Single nucleotide polymorphisms (SNPs) identified in coding regions represent a useful tool for understanding the immune response against pathogens and stressful environmental conditions. In this study, a SNPs database was generated from transcripts involved in the innate immune response of the mussel Mytilus chilensis. The SNPs were identified through hemocytes transcriptome sequencing from 18 individuals, and SNPs mining was performed in 225,336 contigs, yielding 20,306 polymorphisms associated to immune-related genes. Classification of identified SNPs was based on different pathways of the immune response for Mytilus sp. A total of 28 SNPs were identified in the Toll-like receptor pathway and included 5 non-synonymous polymorphisms; 19 SNPs were identified in the apoptosis pathway and included 3 non-synonymous polymorphisms; 35 SNPs were identified in the Ubiquitin-mediated proteolysis pathway and included 4 non-synonymous variants; and 54 SNPs involved in other molecular functions related to the immune response, such as molecular chaperones, antimicrobial peptides, and genes that interacts with marine toxins were also identified. The molecular markers identified in this work could be useful for novel studies, such as those related to associations between high-resolution molecular markers and functional response to pathogen agents.

Authors+Show Affiliations

Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, PO Box 160-C, Concepcion, Chile.No affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

24080470

Citation

Núñez-Acuña, Gustavo, and Cristian Gallardo-Escárate. "Identification of Immune-related SNPs in the Transcriptome of Mytilus Chilensis Through High-throughput Sequencing." Fish & Shellfish Immunology, vol. 35, no. 6, 2013, pp. 1899-905.
Núñez-Acuña G, Gallardo-Escárate C. Identification of immune-related SNPs in the transcriptome of Mytilus chilensis through high-throughput sequencing. Fish Shellfish Immunol. 2013;35(6):1899-905.
Núñez-Acuña, G., & Gallardo-Escárate, C. (2013). Identification of immune-related SNPs in the transcriptome of Mytilus chilensis through high-throughput sequencing. Fish & Shellfish Immunology, 35(6), pp. 1899-905. doi:10.1016/j.fsi.2013.09.028.
Núñez-Acuña G, Gallardo-Escárate C. Identification of Immune-related SNPs in the Transcriptome of Mytilus Chilensis Through High-throughput Sequencing. Fish Shellfish Immunol. 2013;35(6):1899-905. PubMed PMID: 24080470.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Identification of immune-related SNPs in the transcriptome of Mytilus chilensis through high-throughput sequencing. AU - Núñez-Acuña,Gustavo, AU - Gallardo-Escárate,Cristian, Y1 - 2013/09/28/ PY - 2013/08/01/received PY - 2013/09/18/revised PY - 2013/09/19/accepted PY - 2013/10/2/entrez PY - 2013/10/2/pubmed PY - 2014/7/30/medline KW - Immunogenomics KW - Mytilus chilensis KW - RNA-seq KW - SNPs SP - 1899 EP - 905 JF - Fish & shellfish immunology JO - Fish Shellfish Immunol. VL - 35 IS - 6 N2 - Single nucleotide polymorphisms (SNPs) identified in coding regions represent a useful tool for understanding the immune response against pathogens and stressful environmental conditions. In this study, a SNPs database was generated from transcripts involved in the innate immune response of the mussel Mytilus chilensis. The SNPs were identified through hemocytes transcriptome sequencing from 18 individuals, and SNPs mining was performed in 225,336 contigs, yielding 20,306 polymorphisms associated to immune-related genes. Classification of identified SNPs was based on different pathways of the immune response for Mytilus sp. A total of 28 SNPs were identified in the Toll-like receptor pathway and included 5 non-synonymous polymorphisms; 19 SNPs were identified in the apoptosis pathway and included 3 non-synonymous polymorphisms; 35 SNPs were identified in the Ubiquitin-mediated proteolysis pathway and included 4 non-synonymous variants; and 54 SNPs involved in other molecular functions related to the immune response, such as molecular chaperones, antimicrobial peptides, and genes that interacts with marine toxins were also identified. The molecular markers identified in this work could be useful for novel studies, such as those related to associations between high-resolution molecular markers and functional response to pathogen agents. SN - 1095-9947 UR - https://www.unboundmedicine.com/medline/citation/24080470/Identification_of_immune_related_SNPs_in_the_transcriptome_of_Mytilus_chilensis_through_high_throughput_sequencing_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1050-4648(13)00773-0 DB - PRIME DP - Unbound Medicine ER -