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Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals
BACKGROUND: Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Fa...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3751062/ https://www.ncbi.nlm.nih.gov/pubmed/23937070 http://dx.doi.org/10.1186/1471-2164-14-546 |
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author | Pooyaei Mehr, Shaadi F DeSalle, Rob Kao, Hung-Teh Narechania, Apurva Han, Zhou Tchernov, Dan Pieribone, Vincent Gruber, David F |
author_facet | Pooyaei Mehr, Shaadi F DeSalle, Rob Kao, Hung-Teh Narechania, Apurva Han, Zhou Tchernov, Dan Pieribone, Vincent Gruber, David F |
author_sort | Pooyaei Mehr, Shaadi F |
collection | PubMed |
description | BACKGROUND: Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the northern Red Sea. RESULTS: We obtained 80 million 75 bp paired-end cDNA reads from two Favia adult samples collected at 65 m (Fav1, Fav2) on the Illumina GA platform, and generated two de novo assemblies using ABySS and CAP3. After removing redundancy and filtering out low quality reads, our transcriptome datasets contained 58,268 (Fav1) and 62,469 (Fav2) contigs longer than 100 bp, with N50 values of 1,665 bp and 1,439 bp, respectively. Using the proteome of the sea anemone Nematostella vectensis as a reference, we were able to annotate almost 20% of each dataset using reciprocal homology searches. Homologous clustering of these annotated transcripts allowed us to divide them into 7,186 (Fav1) and 6,862 (Fav2) homologous transcript clusters (E-value ≤ 2e(-30)). Functional annotation categories were assigned to homologous clusters using the functional annotation of Nematostella vectensis. General annotation of the assembled transcripts was improved 1-3% using the Acropora digitifera proteome. In addition, we screened these transcript isoform clusters for fluorescent proteins (FPs) homologs and identified seven potential FP homologs in Fav1, and four in Fav2. These transcripts were validated as bona fide FP transcripts via robust fluorescence heterologous expression. Annotation of the assembled contigs revealed that 1.34% and 1.61% (in Fav1 and Fav2, respectively) of the total assembled contigs likely originated from the corals’ algal symbiont, Symbiodinium spp. CONCLUSIONS: Here we present a study to identify the homologous transcript isoform clusters from the transcriptome of Favia corals using a far-related reference proteome. Furthermore, the symbiont-derived transcripts were isolated from the datasets and their contribution quantified. This is the first annotated transcriptome of the genus Favia, a major increase in genomics resources available in this important family of corals. |
format | Online Article Text |
id | pubmed-3751062 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-37510622013-08-24 Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals Pooyaei Mehr, Shaadi F DeSalle, Rob Kao, Hung-Teh Narechania, Apurva Han, Zhou Tchernov, Dan Pieribone, Vincent Gruber, David F BMC Genomics Research Article BACKGROUND: Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the northern Red Sea. RESULTS: We obtained 80 million 75 bp paired-end cDNA reads from two Favia adult samples collected at 65 m (Fav1, Fav2) on the Illumina GA platform, and generated two de novo assemblies using ABySS and CAP3. After removing redundancy and filtering out low quality reads, our transcriptome datasets contained 58,268 (Fav1) and 62,469 (Fav2) contigs longer than 100 bp, with N50 values of 1,665 bp and 1,439 bp, respectively. Using the proteome of the sea anemone Nematostella vectensis as a reference, we were able to annotate almost 20% of each dataset using reciprocal homology searches. Homologous clustering of these annotated transcripts allowed us to divide them into 7,186 (Fav1) and 6,862 (Fav2) homologous transcript clusters (E-value ≤ 2e(-30)). Functional annotation categories were assigned to homologous clusters using the functional annotation of Nematostella vectensis. General annotation of the assembled transcripts was improved 1-3% using the Acropora digitifera proteome. In addition, we screened these transcript isoform clusters for fluorescent proteins (FPs) homologs and identified seven potential FP homologs in Fav1, and four in Fav2. These transcripts were validated as bona fide FP transcripts via robust fluorescence heterologous expression. Annotation of the assembled contigs revealed that 1.34% and 1.61% (in Fav1 and Fav2, respectively) of the total assembled contigs likely originated from the corals’ algal symbiont, Symbiodinium spp. CONCLUSIONS: Here we present a study to identify the homologous transcript isoform clusters from the transcriptome of Favia corals using a far-related reference proteome. Furthermore, the symbiont-derived transcripts were isolated from the datasets and their contribution quantified. This is the first annotated transcriptome of the genus Favia, a major increase in genomics resources available in this important family of corals. BioMed Central 2013-08-12 /pmc/articles/PMC3751062/ /pubmed/23937070 http://dx.doi.org/10.1186/1471-2164-14-546 Text en Copyright © 2013 Pooyaei Mehr et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Pooyaei Mehr, Shaadi F DeSalle, Rob Kao, Hung-Teh Narechania, Apurva Han, Zhou Tchernov, Dan Pieribone, Vincent Gruber, David F Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals |
title | Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals |
title_full | Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals |
title_fullStr | Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals |
title_full_unstemmed | Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals |
title_short | Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals |
title_sort | transcriptome deep-sequencing and clustering of expressed isoforms from favia corals |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3751062/ https://www.ncbi.nlm.nih.gov/pubmed/23937070 http://dx.doi.org/10.1186/1471-2164-14-546 |
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