English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

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.

Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae)