title: Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae).
abstract: 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.
authors.affiliation: Biological Science Department, State University of New York, College at Old Westbury, Old Westbury, NY, 11568, USA. MehrS@oldwestbury.edu.|American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA. MehrS@oldwestbury.edu.
authors.forename: Shaadi
authors.initials: S
authors.lastname: Mehr
authors.affiliation: Baruch College and The Graduate Center, Department of Natural Sciences, City University of New York, New York, NY, 10010, USA. averdes@gradcenter.cuny.edu.
authors.forename: Aida
authors.initials: A
authors.lastname: Verdes
authors.affiliation: American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA. desalle@amnh.org.
authors.forename: Rob
authors.initials: R
authors.lastname: DeSalle
authors.affiliation: American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA. jsparks@amnh.org.|American Museum of Natural History, Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, NY, 10024, USA. jsparks@amnh.org.
authors.forename: John
authors.initials: J
authors.lastname: Sparks
authors.affiliation: John B. Pierce Laboratory, Cellular and Molecular Physiology, Yale University, New Haven, CT 06519, USA. vpieribo@jbpierce.org.
authors.forename: Vincent
authors.initials: V
authors.lastname: Pieribone
authors.affiliation: American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA. David.Gruber@baruch.cuny.edu.|Baruch College and The Graduate Center, Department of Natural Sciences, City University of New York, New York, NY, 10010, USA. David.Gruber@baruch.cuny.edu.
authors.forename: David F
authors.initials: DF
authors.lastname: Gruber
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling / Q000191:economics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000379:methods*; D058977:Molecular Sequence Annotation / Q000379:methods*; D016366:Open Reading Frames; D010802:Phylogeny; D011077:Polychaeta / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000191:economics / Q000379:methods; D015398:Signal Transduction