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Analyses of Expressed Sequence Tags from Chironomus riparius Using Pyrosequencing : Molecular Ecotoxicology Perspective

OBJECTIVES: Chironomus riparius, a non-biting midge (Chironomidae, Diptera), is extensively used as a model organism in aquatic ecotoxicological studies, and considering the potential of C. riparius larvae as a bio-monitoring species, little is known about its genome sequences. This study reports th...

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Autores principales: Nair, Prakash M Gopalakrishnan, Park, Sun Young, Choi, Jinhee
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Korean Society of Environmental Health and Toxicology 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3214979/
https://www.ncbi.nlm.nih.gov/pubmed/22125771
http://dx.doi.org/10.5620/eht.2011.26.e2011010
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author Nair, Prakash M Gopalakrishnan
Park, Sun Young
Choi, Jinhee
author_facet Nair, Prakash M Gopalakrishnan
Park, Sun Young
Choi, Jinhee
author_sort Nair, Prakash M Gopalakrishnan
collection PubMed
description OBJECTIVES: Chironomus riparius, a non-biting midge (Chironomidae, Diptera), is extensively used as a model organism in aquatic ecotoxicological studies, and considering the potential of C. riparius larvae as a bio-monitoring species, little is known about its genome sequences. This study reports the results of an Expressed Sequence Tags (ESTs) sequencing project conducted on C. riparius larvae using 454 pyrosequencing. METHODS: To gain a better understanding of C. riparius transcriptome, we generated ESTs database of C. ripairus using pyrosequencing method. RESULTS: Sequencing runs, using normalized cDNA collections from fourth instar larvae, yielded 20,020 expressed sequence tags, which were assembled into 8,565 contigs and 11,455 singletons. Sequence analysis was performed by BlastX search against the National Center for Biotechnology Information (NCBI) nucleotide (nr) and uniprot protein database. Based on the gene ontology classifications, 24% (E-value ≤1(-5)) of the sequences had known gene functions, 24% had unknown functions and 52% of sequences did not match any known sequences in the existing database. Sequence comparison revealed 81% of the genes have homologous genes among other insects belonging to the order Diptera providing tools for comparative genome analyses. Targeted searches using these annotations identified genes associated with essential metabolic pathways, signaling pathways, detoxification of toxic metabolites and stress response genes of ecotoxicological interest. CONCLUSIONS: The results obtained from this study would eventually make ecotoxicogenomics possible in a truly environmentally relevant species, such as, C. riparius.
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spelling pubmed-32149792011-11-28 Analyses of Expressed Sequence Tags from Chironomus riparius Using Pyrosequencing : Molecular Ecotoxicology Perspective Nair, Prakash M Gopalakrishnan Park, Sun Young Choi, Jinhee Environ Health Toxicol Original Article OBJECTIVES: Chironomus riparius, a non-biting midge (Chironomidae, Diptera), is extensively used as a model organism in aquatic ecotoxicological studies, and considering the potential of C. riparius larvae as a bio-monitoring species, little is known about its genome sequences. This study reports the results of an Expressed Sequence Tags (ESTs) sequencing project conducted on C. riparius larvae using 454 pyrosequencing. METHODS: To gain a better understanding of C. riparius transcriptome, we generated ESTs database of C. ripairus using pyrosequencing method. RESULTS: Sequencing runs, using normalized cDNA collections from fourth instar larvae, yielded 20,020 expressed sequence tags, which were assembled into 8,565 contigs and 11,455 singletons. Sequence analysis was performed by BlastX search against the National Center for Biotechnology Information (NCBI) nucleotide (nr) and uniprot protein database. Based on the gene ontology classifications, 24% (E-value ≤1(-5)) of the sequences had known gene functions, 24% had unknown functions and 52% of sequences did not match any known sequences in the existing database. Sequence comparison revealed 81% of the genes have homologous genes among other insects belonging to the order Diptera providing tools for comparative genome analyses. Targeted searches using these annotations identified genes associated with essential metabolic pathways, signaling pathways, detoxification of toxic metabolites and stress response genes of ecotoxicological interest. CONCLUSIONS: The results obtained from this study would eventually make ecotoxicogenomics possible in a truly environmentally relevant species, such as, C. riparius. The Korean Society of Environmental Health and Toxicology 2011-08-08 /pmc/articles/PMC3214979/ /pubmed/22125771 http://dx.doi.org/10.5620/eht.2011.26.e2011010 Text en © 2011 The Korean Society of Environmental Health and Toxicology http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Nair, Prakash M Gopalakrishnan
Park, Sun Young
Choi, Jinhee
Analyses of Expressed Sequence Tags from Chironomus riparius Using Pyrosequencing : Molecular Ecotoxicology Perspective
title Analyses of Expressed Sequence Tags from Chironomus riparius Using Pyrosequencing : Molecular Ecotoxicology Perspective
title_full Analyses of Expressed Sequence Tags from Chironomus riparius Using Pyrosequencing : Molecular Ecotoxicology Perspective
title_fullStr Analyses of Expressed Sequence Tags from Chironomus riparius Using Pyrosequencing : Molecular Ecotoxicology Perspective
title_full_unstemmed Analyses of Expressed Sequence Tags from Chironomus riparius Using Pyrosequencing : Molecular Ecotoxicology Perspective
title_short Analyses of Expressed Sequence Tags from Chironomus riparius Using Pyrosequencing : Molecular Ecotoxicology Perspective
title_sort analyses of expressed sequence tags from chironomus riparius using pyrosequencing : molecular ecotoxicology perspective
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3214979/
https://www.ncbi.nlm.nih.gov/pubmed/22125771
http://dx.doi.org/10.5620/eht.2011.26.e2011010
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