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

Overview of attention for article published in BMC Genomics, June 2015
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (56th percentile)

Mentioned by

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4 tweeters

Citations

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22 Dimensions

Readers on

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70 Mendeley
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Title
Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae)
Published in
BMC Genomics, June 2015
DOI 10.1186/s12864-015-1565-6
Pubmed ID
Authors

Shaadi Mehr, Aida Verdes, Rob DeSalle, John Sparks, Vincent Pieribone, David F Gruber

Abstract

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. 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. 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.

Twitter Demographics

The data shown below were collected from the profiles of 4 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 70 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 2 3%
Brazil 2 3%
Slovakia 1 1%
United Kingdom 1 1%
Unknown 64 91%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 13 19%
Researcher 11 16%
Student > Bachelor 11 16%
Student > Master 6 9%
Student > Doctoral Student 5 7%
Other 11 16%
Unknown 13 19%
Readers by discipline Count As %
Agricultural and Biological Sciences 35 50%
Biochemistry, Genetics and Molecular Biology 10 14%
Environmental Science 4 6%
Computer Science 2 3%
Immunology and Microbiology 1 1%
Other 3 4%
Unknown 15 21%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 14 June 2015.
All research outputs
#2,953,949
of 7,023,320 outputs
Outputs from BMC Genomics
#2,632
of 5,320 outputs
Outputs of similar age
#89,886
of 216,527 outputs
Outputs of similar age from BMC Genomics
#147
of 226 outputs
Altmetric has tracked 7,023,320 research outputs across all sources so far. This one has received more attention than most of these and is in the 56th percentile.
So far Altmetric has tracked 5,320 research outputs from this source. They receive a mean Attention Score of 4.0. This one is in the 47th percentile – i.e., 47% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 216,527 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 56% of its contemporaries.
We're also able to compare this research output to 226 others from the same source and published within six weeks on either side of this one. This one is in the 29th percentile – i.e., 29% of its contemporaries scored the same or lower than it.