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

Mehr S, Verdes A, DeSalle R, Sparks J, Pieribone V, Gruber DF - BMC Genomics (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Biological Science Department, State University of New York, College at Old Westbury, Old Westbury, NY, 11568, USA. MehrS@oldwestbury.edu.

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.

No MeSH data available.


Related in: MedlinePlus

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).
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Fig7: 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).

Mentions: Within annelid polychaetes there are a number of bioluminescent species distributed in various families such as Acrocirridae (Swima), Chaetopteridae (Chaetopterus), Flabelligeridae (Poeobius, Flota), Polynoidae (Harmothoe, Polynoe), Syllidae (Odontosyllis, Eusyllis, Pionosyllis), Terebellidae (Polycirrus, Thelepus) and Tomopteridae (Tomopteris) [66]. To date, no bioluminescent protein sequence has been reported from this phylum, but we do report homologous sequences of a luciferase protein (Figure 5). The fact that the putative Hermodice carunculata luciferase shows highest homology to the luciferase of a phylogenetically distant cnidarian (Renilla reniformis) can probably be attributable to the lack of publicly available luciferase sequences from more closely related organisms. The transcriptomic dataset presented herein can greatly help identify and characterize this putative photoprotein and facilitate future studies investigating the genetic and biochemical basis of light production in annelids. In addition, we report both green and red biofluorescence in Hermodice carunculata, yet the search of the genome showed no homology to any known fluorescent protein species (Figure 7).Figure 7


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

Mehr S, Verdes A, DeSalle R, Sparks J, Pieribone V, Gruber DF - BMC Genomics (2015)

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).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4462082&req=5

Fig7: 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).
Mentions: Within annelid polychaetes there are a number of bioluminescent species distributed in various families such as Acrocirridae (Swima), Chaetopteridae (Chaetopterus), Flabelligeridae (Poeobius, Flota), Polynoidae (Harmothoe, Polynoe), Syllidae (Odontosyllis, Eusyllis, Pionosyllis), Terebellidae (Polycirrus, Thelepus) and Tomopteridae (Tomopteris) [66]. To date, no bioluminescent protein sequence has been reported from this phylum, but we do report homologous sequences of a luciferase protein (Figure 5). The fact that the putative Hermodice carunculata luciferase shows highest homology to the luciferase of a phylogenetically distant cnidarian (Renilla reniformis) can probably be attributable to the lack of publicly available luciferase sequences from more closely related organisms. The transcriptomic dataset presented herein can greatly help identify and characterize this putative photoprotein and facilitate future studies investigating the genetic and biochemical basis of light production in annelids. In addition, we report both green and red biofluorescence in Hermodice carunculata, yet the search of the genome showed no homology to any known fluorescent protein species (Figure 7).Figure 7

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Biological Science Department, State University of New York, College at Old Westbury, Old Westbury, NY, 11568, USA. MehrS@oldwestbury.edu.

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.

No MeSH data available.


Related in: MedlinePlus