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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

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.
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Fig2: 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.

Mentions: For comparative annotation, all ORFs longer than 200 AA (58,454) were initially searched against two existing annelid genomic datasets, Capitella teleta (http://genome.jgi-psf.org/Capca1/Capca1.home.html) and Helobdella robusta (http://genome.jgi-psf.org/Helro1/Helro1.home.html); and subsequently against Paramphinome jeffreysi and Eurythoe complanata, using BlastP [40] with a significant E-value of 2e−15. Similarity search showed that 23,617 (40.5%) ORFs have similarity higher than 70% against C. teleta, while 20,468 (35%) ORFs have similarity higher than 70% against H. robusta (Figure 2). This indicates that the proportion of sequences with matches in the proteome of C. teleta is greater than the proportion of matches for H. robusta. This is expected, as C. teleta and H. carunculata are both polychaete annelids, as opposed to H. robusta, a leech (Clitellata). In total, 15,841 transcripts had a significant hit (70% length homology) in both datasets. Furthermore, 29,819 of these ORFs showed homology to P. jeffreysi and 36,033 to E. complanata. Of these ORFs, 23,441 were homologous to both Paramphinome jeffreysi and Eurythoe complanata. These shared sequences can be used for future genome annotation of both annelids and amphinomids, respectively (data available upon request).Figure 2


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)

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

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

Fig2: 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.
Mentions: For comparative annotation, all ORFs longer than 200 AA (58,454) were initially searched against two existing annelid genomic datasets, Capitella teleta (http://genome.jgi-psf.org/Capca1/Capca1.home.html) and Helobdella robusta (http://genome.jgi-psf.org/Helro1/Helro1.home.html); and subsequently against Paramphinome jeffreysi and Eurythoe complanata, using BlastP [40] with a significant E-value of 2e−15. Similarity search showed that 23,617 (40.5%) ORFs have similarity higher than 70% against C. teleta, while 20,468 (35%) ORFs have similarity higher than 70% against H. robusta (Figure 2). This indicates that the proportion of sequences with matches in the proteome of C. teleta is greater than the proportion of matches for H. robusta. This is expected, as C. teleta and H. carunculata are both polychaete annelids, as opposed to H. robusta, a leech (Clitellata). In total, 15,841 transcripts had a significant hit (70% length homology) in both datasets. Furthermore, 29,819 of these ORFs showed homology to P. jeffreysi and 36,033 to E. complanata. Of these ORFs, 23,441 were homologous to both Paramphinome jeffreysi and Eurythoe complanata. These shared sequences can be used for future genome annotation of both annelids and amphinomids, respectively (data available upon request).Figure 2

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