Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo(a)pyrene and phenanthrene
Autor(a) principal: | |
---|---|
Data de Publicação: | 2013 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional do INPA |
Texto Completo: | https://repositorio.inpa.gov.br/handle/1/14716 |
Resumo: | This study aims to evaluate the transcriptome alterations, through cDNA libraries, associated with the combined effects of two PAHs, benzo[a]pyrene (0.5 μg/L) and phenanthrene (50 μg/L), present in crude oil, on specimens of Symphysodon aequifasciatus (discus fish) after 48 h of exposure. The cDNA libraries were constructed according to the SOLiD™ SAGE™ protocol for sequencing in the SOLiD v.3 Plus sequencer. The results were analyzed by bioinformatics and differentially expressed genes were categorized using the gene ontology program. The functional categories (terms) found in the gene ontology and the gene network generated using STRING software were used to predict the adverse effects of benzo[a]pyrene and phenanthrene in the liver. In the present study, 27,127 genes (compared to Danio rerio database) were identified. Considering only those genes with a p-value less than or equal to 0.05 and greater than or equal to two-fold change in expression across libraries, we found 804 genes, 438 down-regulated (54%) and 366 up-regulated (46%), in the experimental group compared to the control. Out of this total, 327 genes were successfully categorized, 174 downregulated and 153 up-regulated, using gene ontology. Using String, the gene network was composed by 199 nodes, 124 of them resulting in 274 interactions. The results showed that even an acute exposure of 48 h caused metabolic change in response to environmental contaminants, resulting in changes of cell integrity, in oxidation-reduction processes, in the immune response and disturbances of intracellular signaling of discus fish. Also the gene network has showed no central interplay cluster, exhibiting instead interconnected clusters interactions and connected sub-networks. These findings highlight that even an acute sublethal exposure of PAHs can cause metabolism changes that may affect survival of discus. Our findings using SOLiD coupled with SAGE-method resulted in a powerful and reliable means for gene expression analysis in discus, a non-model Amazonian fish. © 2013 Lemgruber et al. |
id |
INPA-2_286d4c00d8ddf8827da373a7b24631ab |
---|---|
oai_identifier_str |
oai:repositorio:1/14716 |
network_acronym_str |
INPA-2 |
network_name_str |
Repositório Institucional do INPA |
repository_id_str |
|
spelling |
Souza Pinto Lemgruber, Renato deMarshall, Nislanha Ana dos AnjosAndrea, Ghelfi,Fagundes, Daniel BarrosVal, Adalberto Luis2020-04-24T17:00:47Z2020-04-24T17:00:47Z2013https://repositorio.inpa.gov.br/handle/1/1471610.1371/journal.pone.0081083This study aims to evaluate the transcriptome alterations, through cDNA libraries, associated with the combined effects of two PAHs, benzo[a]pyrene (0.5 μg/L) and phenanthrene (50 μg/L), present in crude oil, on specimens of Symphysodon aequifasciatus (discus fish) after 48 h of exposure. The cDNA libraries were constructed according to the SOLiD™ SAGE™ protocol for sequencing in the SOLiD v.3 Plus sequencer. The results were analyzed by bioinformatics and differentially expressed genes were categorized using the gene ontology program. The functional categories (terms) found in the gene ontology and the gene network generated using STRING software were used to predict the adverse effects of benzo[a]pyrene and phenanthrene in the liver. In the present study, 27,127 genes (compared to Danio rerio database) were identified. Considering only those genes with a p-value less than or equal to 0.05 and greater than or equal to two-fold change in expression across libraries, we found 804 genes, 438 down-regulated (54%) and 366 up-regulated (46%), in the experimental group compared to the control. Out of this total, 327 genes were successfully categorized, 174 downregulated and 153 up-regulated, using gene ontology. Using String, the gene network was composed by 199 nodes, 124 of them resulting in 274 interactions. The results showed that even an acute exposure of 48 h caused metabolic change in response to environmental contaminants, resulting in changes of cell integrity, in oxidation-reduction processes, in the immune response and disturbances of intracellular signaling of discus fish. Also the gene network has showed no central interplay cluster, exhibiting instead interconnected clusters interactions and connected sub-networks. These findings highlight that even an acute sublethal exposure of PAHs can cause metabolism changes that may affect survival of discus. Our findings using SOLiD coupled with SAGE-method resulted in a powerful and reliable means for gene expression analysis in discus, a non-model Amazonian fish. © 2013 Lemgruber et al.Volume 8, Número 12Attribution-NonCommercial-NoDerivs 3.0 Brazilhttp://creativecommons.org/licenses/by-nc-nd/3.0/br/info:eu-repo/semantics/openAccessBenzo(a)pyreneDna, ComplementaryPhenanthreneTranscriptomeAmino Acid SequenceControlled StudyDna BindingDna LibraryDown RegulationEnvironmental ExposureGene ExpressionGene FunctionGene IdentificationGene InteractionGene OntologyHigh Throughput SequencingNonhumanOxidation Reduction ReactionPerciformesRna ExtractionSerial Analysis Of Gene ExpressionSymphysodon AequifasciatusUp-regulationAnimalssBenzo(a)pyreneCichlidsFish ProteinsGene Expression RegulationPhenanthrenesTranscriptomeFunctional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo(a)pyrene and phenanthreneinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlePLoS ONEengreponame:Repositório Institucional do INPAinstname:Instituto Nacional de Pesquisas da Amazônia (INPA)instacron:INPAORIGINALartigo-inpa.pdfapplication/pdf1692933https://repositorio.inpa.gov.br/bitstream/1/14716/1/artigo-inpa.pdf6c587807ea551794a26558f1a602a665MD51CC-LICENSElicense_rdfapplication/octet-stream914https://repositorio.inpa.gov.br/bitstream/1/14716/2/license_rdf4d2950bda3d176f570a9f8b328dfbbefMD521/147162020-07-14 10:16:38.044oai:repositorio:1/14716Repositório de PublicaçõesPUBhttps://repositorio.inpa.gov.br/oai/requestopendoar:2020-07-14T14:16:38Repositório Institucional do INPA - Instituto Nacional de Pesquisas da Amazônia (INPA)false |
dc.title.en.fl_str_mv |
Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo(a)pyrene and phenanthrene |
title |
Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo(a)pyrene and phenanthrene |
spellingShingle |
Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo(a)pyrene and phenanthrene Souza Pinto Lemgruber, Renato de Benzo(a)pyrene Dna, Complementary Phenanthrene Transcriptome Amino Acid Sequence Controlled Study Dna Binding Dna Library Down Regulation Environmental Exposure Gene Expression Gene Function Gene Identification Gene Interaction Gene Ontology High Throughput Sequencing Nonhuman Oxidation Reduction Reaction Perciformes Rna Extraction Serial Analysis Of Gene Expression Symphysodon Aequifasciatus Up-regulation Animalss Benzo(a)pyrene Cichlids Fish Proteins Gene Expression Regulation Phenanthrenes Transcriptome |
title_short |
Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo(a)pyrene and phenanthrene |
title_full |
Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo(a)pyrene and phenanthrene |
title_fullStr |
Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo(a)pyrene and phenanthrene |
title_full_unstemmed |
Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo(a)pyrene and phenanthrene |
title_sort |
Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo(a)pyrene and phenanthrene |
author |
Souza Pinto Lemgruber, Renato de |
author_facet |
Souza Pinto Lemgruber, Renato de Marshall, Nislanha Ana dos Anjos Andrea, Ghelfi, Fagundes, Daniel Barros Val, Adalberto Luis |
author_role |
author |
author2 |
Marshall, Nislanha Ana dos Anjos Andrea, Ghelfi, Fagundes, Daniel Barros Val, Adalberto Luis |
author2_role |
author author author author |
dc.contributor.author.fl_str_mv |
Souza Pinto Lemgruber, Renato de Marshall, Nislanha Ana dos Anjos Andrea, Ghelfi, Fagundes, Daniel Barros Val, Adalberto Luis |
dc.subject.eng.fl_str_mv |
Benzo(a)pyrene Dna, Complementary Phenanthrene Transcriptome Amino Acid Sequence Controlled Study Dna Binding Dna Library Down Regulation Environmental Exposure Gene Expression Gene Function Gene Identification Gene Interaction Gene Ontology High Throughput Sequencing Nonhuman Oxidation Reduction Reaction Perciformes Rna Extraction Serial Analysis Of Gene Expression Symphysodon Aequifasciatus Up-regulation Animalss Benzo(a)pyrene Cichlids Fish Proteins Gene Expression Regulation Phenanthrenes Transcriptome |
topic |
Benzo(a)pyrene Dna, Complementary Phenanthrene Transcriptome Amino Acid Sequence Controlled Study Dna Binding Dna Library Down Regulation Environmental Exposure Gene Expression Gene Function Gene Identification Gene Interaction Gene Ontology High Throughput Sequencing Nonhuman Oxidation Reduction Reaction Perciformes Rna Extraction Serial Analysis Of Gene Expression Symphysodon Aequifasciatus Up-regulation Animalss Benzo(a)pyrene Cichlids Fish Proteins Gene Expression Regulation Phenanthrenes Transcriptome |
description |
This study aims to evaluate the transcriptome alterations, through cDNA libraries, associated with the combined effects of two PAHs, benzo[a]pyrene (0.5 μg/L) and phenanthrene (50 μg/L), present in crude oil, on specimens of Symphysodon aequifasciatus (discus fish) after 48 h of exposure. The cDNA libraries were constructed according to the SOLiD™ SAGE™ protocol for sequencing in the SOLiD v.3 Plus sequencer. The results were analyzed by bioinformatics and differentially expressed genes were categorized using the gene ontology program. The functional categories (terms) found in the gene ontology and the gene network generated using STRING software were used to predict the adverse effects of benzo[a]pyrene and phenanthrene in the liver. In the present study, 27,127 genes (compared to Danio rerio database) were identified. Considering only those genes with a p-value less than or equal to 0.05 and greater than or equal to two-fold change in expression across libraries, we found 804 genes, 438 down-regulated (54%) and 366 up-regulated (46%), in the experimental group compared to the control. Out of this total, 327 genes were successfully categorized, 174 downregulated and 153 up-regulated, using gene ontology. Using String, the gene network was composed by 199 nodes, 124 of them resulting in 274 interactions. The results showed that even an acute exposure of 48 h caused metabolic change in response to environmental contaminants, resulting in changes of cell integrity, in oxidation-reduction processes, in the immune response and disturbances of intracellular signaling of discus fish. Also the gene network has showed no central interplay cluster, exhibiting instead interconnected clusters interactions and connected sub-networks. These findings highlight that even an acute sublethal exposure of PAHs can cause metabolism changes that may affect survival of discus. Our findings using SOLiD coupled with SAGE-method resulted in a powerful and reliable means for gene expression analysis in discus, a non-model Amazonian fish. © 2013 Lemgruber et al. |
publishDate |
2013 |
dc.date.issued.fl_str_mv |
2013 |
dc.date.accessioned.fl_str_mv |
2020-04-24T17:00:47Z |
dc.date.available.fl_str_mv |
2020-04-24T17:00:47Z |
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 |
https://repositorio.inpa.gov.br/handle/1/14716 |
dc.identifier.doi.none.fl_str_mv |
10.1371/journal.pone.0081083 |
url |
https://repositorio.inpa.gov.br/handle/1/14716 |
identifier_str_mv |
10.1371/journal.pone.0081083 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartof.pt_BR.fl_str_mv |
Volume 8, Número 12 |
dc.rights.driver.fl_str_mv |
Attribution-NonCommercial-NoDerivs 3.0 Brazil http://creativecommons.org/licenses/by-nc-nd/3.0/br/ info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
Attribution-NonCommercial-NoDerivs 3.0 Brazil http://creativecommons.org/licenses/by-nc-nd/3.0/br/ |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
PLoS ONE |
publisher.none.fl_str_mv |
PLoS ONE |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional do INPA instname:Instituto Nacional de Pesquisas da Amazônia (INPA) instacron:INPA |
instname_str |
Instituto Nacional de Pesquisas da Amazônia (INPA) |
instacron_str |
INPA |
institution |
INPA |
reponame_str |
Repositório Institucional do INPA |
collection |
Repositório Institucional do INPA |
bitstream.url.fl_str_mv |
https://repositorio.inpa.gov.br/bitstream/1/14716/1/artigo-inpa.pdf https://repositorio.inpa.gov.br/bitstream/1/14716/2/license_rdf |
bitstream.checksum.fl_str_mv |
6c587807ea551794a26558f1a602a665 4d2950bda3d176f570a9f8b328dfbbef |
bitstream.checksumAlgorithm.fl_str_mv |
MD5 MD5 |
repository.name.fl_str_mv |
Repositório Institucional do INPA - Instituto Nacional de Pesquisas da Amazônia (INPA) |
repository.mail.fl_str_mv |
|
_version_ |
1809928896489979904 |