Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals

Shaadi F. Pooyaei Mehr, Rob DeSalle, Hung Teh Kao, Apurva Narechania, Zhou Han, Dan Tchernov, Vincent Pieribone, David F. Gruber

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Article number546
JournalBMC Genomics
Issue number1
StatePublished - 12 Aug 2013

Bibliographical note

Funding Information:
We thank Timor Katz and Tali Mass of the Interuniversity Institute of Eilat for their technical diving assistance in the collection of coral samples. Coral sample collections in this study have complied with the current laws of Israeli Natural Parks Authority; permit 2010/38008. Funding was provided by NSF grant # 0920572 and via a Baruch College Travel Grant to DFG.


  • Blast
  • Clustering
  • Contig
  • Coral
  • Fluorescent protein
  • High-throughput sequencing
  • Illumina paired-end
  • K-mer
  • Open reading frame

ASJC Scopus subject areas

  • Biotechnology
  • Genetics


Dive into the research topics of 'Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals'. Together they form a unique fingerprint.

Cite this