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.

Figure 1

Assembled contig length distribution. Each number on top of each bar represents number of assembled contigs per length category.

Figure 2

Venn diagram distribution of similarity search results for Hermodice carunculata. Based on 58,454 predicted Open Reading Frames (ORFs) of genes longer than 200 amino acids. The number of unique sequence-based annotation is the best sum of unique BlastP hits (E-value of 2e⁻¹⁵) from Capitella teleta and Helobdella robusta proteome, respectively.

Figure 3

Functional annotation of Hermodice carunculata transcripts. The 30 most abundant GOslim terms based on A molecular function, B biological processes, C cellular component.

Figure 4

Percentage of functionally annotated transcripts relative to their length.

Figure 5

Overlapping region of amino acid sequence alignment of homologous proteins sequences to luciferase from the sea pansy, Renilla sp.

Figure 6

Maximum likelihood tree of 21 Attractin proteins and one newly identified attractin sequence from Hermodice carunculata. The newly identified attractin is colored red.

Figure 7

Fluorescent macro image of Hermodice carunculata using 450–500 nm excitation and 514 nm LP emission (A); white light image (B); and fluorescent macro comparison (using 450-500 nm excitation and 514nmLP emission) (C); confocal images (D- G) obtained with a Olympus Fluoview FV1000 (Olympus, Japan) confocal laser scanning microscope using an Olympus LUMFL 60×/1.10 W objective (excitation 488 nm wavelength Ar-laser was used), illustrating distrubution of green and red fluorescence; (H) Emission spectra using an Ocean Optics USB2000+ miniature spectrometer (Dunedin, FL) equipped with a hand-held fiber optic probe (Ocean Optics ZFQ-12135).