Uncovering the immunological repertoire of the carpet shell clam Ruditapes decussatus through a transcriptomic-based approach

Detalhes bibliográficos
Autor(a) principal: Batista, Frederico
Data de Publicação: 2019
Outros Autores: Churcher, Allison, Manchado, Manuel, Leitão, Alexandra, Power, Deborah
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10400.1/14589
Resumo: The grooved carpet-shell clam Ruditapes decussatus is native to the Northern Atlantic and Mediterranean Sea and has a high commercial value. It is one of the main native bivalve species cultured in Europe. The main objective of the present study was to gain further insights into the immunological repertoire of R. decussatus through a transcriptomic approach. Pooled mantle samples of eight R. decussatus individuals were sequenced using Illumina platform. A total of 67 132 contigs with more than 800 bp were obtained. Manual annotation of these contigs revealed 146 immune-related genes. The gene families in which the highest number of immune-related genes was observed were: C1q domain-containing proteins (63), tumor necrosis factors (15) and toll-like receptors (TLRs, 10). A total of 5 359 putative single nucleotide polymorphisms (SNPs) were identified in the 146 immune-related genes. The density of SNPs ranged between 0.04 and 7.92 SNPs/100 bp. The highest and the lowest SNP density were observed in genes of the C1q domain-containing protein family. Due to the importance of TLRs in innate immunity, we focused our attention on these membrane receptors. Ten TLRs were identified based on protein domain organization. Phylogenetic analysis revealed that R. decussatus TLRs were diverse and only 3 showed orthology with TLRs of known immune functions in other bivalve species. Moreover, our analysis suggests that lineage restricted-expansions of TLRs occurred in all mollusc taxa analysed including in venerids.
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spelling Uncovering the immunological repertoire of the carpet shell clam Ruditapes decussatus through a transcriptomic-based approachRuditapes decussatusTranscriptomeImmune genesToll-like receptorsThe grooved carpet-shell clam Ruditapes decussatus is native to the Northern Atlantic and Mediterranean Sea and has a high commercial value. It is one of the main native bivalve species cultured in Europe. The main objective of the present study was to gain further insights into the immunological repertoire of R. decussatus through a transcriptomic approach. Pooled mantle samples of eight R. decussatus individuals were sequenced using Illumina platform. A total of 67 132 contigs with more than 800 bp were obtained. Manual annotation of these contigs revealed 146 immune-related genes. The gene families in which the highest number of immune-related genes was observed were: C1q domain-containing proteins (63), tumor necrosis factors (15) and toll-like receptors (TLRs, 10). A total of 5 359 putative single nucleotide polymorphisms (SNPs) were identified in the 146 immune-related genes. The density of SNPs ranged between 0.04 and 7.92 SNPs/100 bp. The highest and the lowest SNP density were observed in genes of the C1q domain-containing protein family. Due to the importance of TLRs in innate immunity, we focused our attention on these membrane receptors. Ten TLRs were identified based on protein domain organization. Phylogenetic analysis revealed that R. decussatus TLRs were diverse and only 3 showed orthology with TLRs of known immune functions in other bivalve species. Moreover, our analysis suggests that lineage restricted-expansions of TLRs occurred in all mollusc taxa analysed including in venerids.This study was financially supported by the projects: AQUAGENET (SOE2/P1/E287) funded by the European Regional Development Fund within the program INTERREG IVB SUDOE; COMPETE/FEDER (FCOMP-01-0124-FEDER-010607); PTDC/MAR/103550/2008 and CCMAR/Multi/04326/2013 funded by the Foundation for Science and Technology (FCT). F.M.B. and A.M.C were supported by postdoctoral fellowship grants from FCT (SFRH/BPD/108591/2015 and SFRH/BPD/85408/2012).ElsevierSapientiaBatista, FredericoChurcher, AllisonManchado, ManuelLeitão, AlexandraPower, Deborah2020-08-03T16:19:32Z20192019-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.1/14589eng10.1016/j.aaf.2018.03.003info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-24T10:26:54Zoai:sapientia.ualg.pt:10400.1/14589Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T20:05:36.333871Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Uncovering the immunological repertoire of the carpet shell clam Ruditapes decussatus through a transcriptomic-based approach
title Uncovering the immunological repertoire of the carpet shell clam Ruditapes decussatus through a transcriptomic-based approach
spellingShingle Uncovering the immunological repertoire of the carpet shell clam Ruditapes decussatus through a transcriptomic-based approach
Batista, Frederico
Ruditapes decussatus
Transcriptome
Immune genes
Toll-like receptors
title_short Uncovering the immunological repertoire of the carpet shell clam Ruditapes decussatus through a transcriptomic-based approach
title_full Uncovering the immunological repertoire of the carpet shell clam Ruditapes decussatus through a transcriptomic-based approach
title_fullStr Uncovering the immunological repertoire of the carpet shell clam Ruditapes decussatus through a transcriptomic-based approach
title_full_unstemmed Uncovering the immunological repertoire of the carpet shell clam Ruditapes decussatus through a transcriptomic-based approach
title_sort Uncovering the immunological repertoire of the carpet shell clam Ruditapes decussatus through a transcriptomic-based approach
author Batista, Frederico
author_facet Batista, Frederico
Churcher, Allison
Manchado, Manuel
Leitão, Alexandra
Power, Deborah
author_role author
author2 Churcher, Allison
Manchado, Manuel
Leitão, Alexandra
Power, Deborah
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Sapientia
dc.contributor.author.fl_str_mv Batista, Frederico
Churcher, Allison
Manchado, Manuel
Leitão, Alexandra
Power, Deborah
dc.subject.por.fl_str_mv Ruditapes decussatus
Transcriptome
Immune genes
Toll-like receptors
topic Ruditapes decussatus
Transcriptome
Immune genes
Toll-like receptors
description The grooved carpet-shell clam Ruditapes decussatus is native to the Northern Atlantic and Mediterranean Sea and has a high commercial value. It is one of the main native bivalve species cultured in Europe. The main objective of the present study was to gain further insights into the immunological repertoire of R. decussatus through a transcriptomic approach. Pooled mantle samples of eight R. decussatus individuals were sequenced using Illumina platform. A total of 67 132 contigs with more than 800 bp were obtained. Manual annotation of these contigs revealed 146 immune-related genes. The gene families in which the highest number of immune-related genes was observed were: C1q domain-containing proteins (63), tumor necrosis factors (15) and toll-like receptors (TLRs, 10). A total of 5 359 putative single nucleotide polymorphisms (SNPs) were identified in the 146 immune-related genes. The density of SNPs ranged between 0.04 and 7.92 SNPs/100 bp. The highest and the lowest SNP density were observed in genes of the C1q domain-containing protein family. Due to the importance of TLRs in innate immunity, we focused our attention on these membrane receptors. Ten TLRs were identified based on protein domain organization. Phylogenetic analysis revealed that R. decussatus TLRs were diverse and only 3 showed orthology with TLRs of known immune functions in other bivalve species. Moreover, our analysis suggests that lineage restricted-expansions of TLRs occurred in all mollusc taxa analysed including in venerids.
publishDate 2019
dc.date.none.fl_str_mv 2019
2019-01-01T00:00:00Z
2020-08-03T16:19:32Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
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dc.identifier.uri.fl_str_mv http://hdl.handle.net/10400.1/14589
url http://hdl.handle.net/10400.1/14589
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 10.1016/j.aaf.2018.03.003
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dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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