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Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae)
BACKGROUND: The amphinomid polychaete Hermodice carunculata is a cosmopolitan and ecologically important omnivore in coral reef ecosystems, preying on a diverse suite of reef organisms and potentially acting as a vector for coral disease. While amphinomids are a key group for determining the root of...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4462082/ https://www.ncbi.nlm.nih.gov/pubmed/26059236 http://dx.doi.org/10.1186/s12864-015-1565-6 |
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author | Mehr, Shaadi Verdes, Aida DeSalle, Rob Sparks, John Pieribone, Vincent Gruber, David F |
author_facet | Mehr, Shaadi Verdes, Aida DeSalle, Rob Sparks, John Pieribone, Vincent Gruber, David F |
author_sort | Mehr, Shaadi |
collection | PubMed |
description | BACKGROUND: The amphinomid polychaete Hermodice carunculata is a cosmopolitan and ecologically important omnivore in coral reef ecosystems, preying on a diverse suite of reef organisms and potentially acting as a vector for coral disease. While amphinomids are a key group for determining the root of the Annelida, their phylogenetic position has been difficult to resolve, and their publically available genomic data was scarce. RESULTS: We performed deep transcriptome sequencing (Illumina HiSeq) and profiling on Hermodice carunculata collected in the Western Atlantic Ocean. We focused this study on 58,454 predicted Open Reading Frames (ORFs) of genes longer than 200 amino acids for our homology search, and Gene Ontology (GO) terms and InterPro IDs were assigned to 32,500 of these ORFs. We used this de novo assembled transcriptome to recover major signaling pathways and housekeeping genes. We also identify a suite of H. carunculata genes related to reproduction and immune response. CONCLUSIONS: We provide a comprehensive catalogue of annotated genes for Hermodice carunculata and expand the knowledge of reproduction and immune response genes in annelids, in general. Overall, this study vastly expands the available genomic data for H. carunculata, of which previously consisted of only 279 nucleotide sequences in NCBI. This underscores the utility of Illumina sequencing for de novo transcriptome assembly in non-model organisms as a cost-effective and efficient tool for gene discovery and downstream applications, such as phylogenetic analysis and gene expression profiling. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1565-6) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4462082 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-44620822015-06-11 Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae) Mehr, Shaadi Verdes, Aida DeSalle, Rob Sparks, John Pieribone, Vincent Gruber, David F BMC Genomics Research Article BACKGROUND: The amphinomid polychaete Hermodice carunculata is a cosmopolitan and ecologically important omnivore in coral reef ecosystems, preying on a diverse suite of reef organisms and potentially acting as a vector for coral disease. While amphinomids are a key group for determining the root of the Annelida, their phylogenetic position has been difficult to resolve, and their publically available genomic data was scarce. RESULTS: We performed deep transcriptome sequencing (Illumina HiSeq) and profiling on Hermodice carunculata collected in the Western Atlantic Ocean. We focused this study on 58,454 predicted Open Reading Frames (ORFs) of genes longer than 200 amino acids for our homology search, and Gene Ontology (GO) terms and InterPro IDs were assigned to 32,500 of these ORFs. We used this de novo assembled transcriptome to recover major signaling pathways and housekeeping genes. We also identify a suite of H. carunculata genes related to reproduction and immune response. CONCLUSIONS: We provide a comprehensive catalogue of annotated genes for Hermodice carunculata and expand the knowledge of reproduction and immune response genes in annelids, in general. Overall, this study vastly expands the available genomic data for H. carunculata, of which previously consisted of only 279 nucleotide sequences in NCBI. This underscores the utility of Illumina sequencing for de novo transcriptome assembly in non-model organisms as a cost-effective and efficient tool for gene discovery and downstream applications, such as phylogenetic analysis and gene expression profiling. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1565-6) contains supplementary material, which is available to authorized users. BioMed Central 2015-06-10 /pmc/articles/PMC4462082/ /pubmed/26059236 http://dx.doi.org/10.1186/s12864-015-1565-6 Text en © Mehr et al. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Mehr, Shaadi Verdes, Aida DeSalle, Rob Sparks, John Pieribone, Vincent Gruber, David F Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae) |
title | Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae) |
title_full | Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae) |
title_fullStr | Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae) |
title_full_unstemmed | Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae) |
title_short | Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae) |
title_sort | transcriptome sequencing and annotation of the polychaete hermodice carunculata (annelida, amphinomidae) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4462082/ https://www.ncbi.nlm.nih.gov/pubmed/26059236 http://dx.doi.org/10.1186/s12864-015-1565-6 |
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