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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

Assembled contig length distribution. Each number on top of each bar represents number of assembled contigs per length category.
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Fig1: Assembled contig length distribution. Each number on top of each bar represents number of assembled contigs per length category.

Mentions: Assemblies at higher k-mers (e.g. 41–55) had lower mean length and N50 than assemblies at lower k-mers (21–35) (Table 1). This is in agreement with other summary statistics of NGS reported de novo assembly data [38]. The lower N50 and mean in the final merged dataset, compared with k-mer 51 and k-mer 55, is due to addition of shorter sequences from lower k-mer assemblies. As outlined in Table 1, the N50 has changed from 584 in k-mer 21 to 1095 bp in the merged set of contigs, indicating an improvement in the assembly contig length. Although the majority of the contig length is between 200–600 bp, we obtained 20,828 contigs, with length greater than 3,563 bp (Figure 1). This result indicates that the data has a very high quality for further annotation. Lastly, the assembled sequences were deposited in Transcriptome Shotgun Assembly (TSA) at the NCBI.Figure 1


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)

Assembled contig length distribution. Each number on top of each bar represents number of assembled contigs per length category.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: Assembled contig length distribution. Each number on top of each bar represents number of assembled contigs per length category.
Mentions: Assemblies at higher k-mers (e.g. 41–55) had lower mean length and N50 than assemblies at lower k-mers (21–35) (Table 1). This is in agreement with other summary statistics of NGS reported de novo assembly data [38]. The lower N50 and mean in the final merged dataset, compared with k-mer 51 and k-mer 55, is due to addition of shorter sequences from lower k-mer assemblies. As outlined in Table 1, the N50 has changed from 584 in k-mer 21 to 1095 bp in the merged set of contigs, indicating an improvement in the assembly contig length. Although the majority of the contig length is between 200–600 bp, we obtained 20,828 contigs, with length greater than 3,563 bp (Figure 1). This result indicates that the data has a very high quality for further annotation. Lastly, the assembled sequences were deposited in Transcriptome Shotgun Assembly (TSA) at the NCBI.Figure 1

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