Uncovering the immunological repertoire of the carpet shell clam Ruditapes decussatus through a transcriptomic-based approach
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , |
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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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 |
format |
article |
status_str |
publishedVersion |
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 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
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 instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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 |
repository.mail.fl_str_mv |
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1799133296016228352 |