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OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

Overview of attention for article published in BMC Genomics, August 2016
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  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (70th percentile)
  • Good Attention Score compared to outputs of the same age and source (76th percentile)

Mentioned by

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9 tweeters

Citations

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17 Dimensions

Readers on

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36 Mendeley
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Title
OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis
Published in
BMC Genomics, August 2016
DOI 10.1186/s12864-016-2886-9
Pubmed ID
Authors

Alfredo Rago, Donald G. Gilbert, Jeong-Hyeon Choi, Timothy B. Sackton, Xu Wang, Yogeshwar D. Kelkar, John H. Werren, John K. Colbourne

Abstract

Nasonia vitripennis is an emerging insect model system with haplodiploid genetics. It holds a key position within the insect phylogeny for comparative, evolutionary and behavioral genetic studies. The draft genomes for N. vitripennis and two sibling species were published in 2010, yet a considerable amount of transcriptiome data have since been produced thereby enabling improvements to the original (OGS1.2) annotated gene set. We describe and apply the EvidentialGene method used to produce an updated gene set (OGS2). We also carry out comparative analyses showcasing the usefulness of the revised annotated gene set. The revised annotation (OGS2) now consists of 24,388 genes with supporting evidence, compared to 18,850 for OGS1.2. Improvements include the nearly complete annotation of untranslated regions (UTR) for 97 % of the genes compared to 28 % of genes for OGS1.2. The fraction of RNA-Seq validated introns also grow from 85 to 98 % in this latest gene set. The EST and RNA-Seq expression data provide support for several non-protein coding loci and 7712 alternative transcripts for 4146 genes. Notably, we report 180 alternative transcripts for the gene lola. Nasonia now has among the most complete insect gene set; only 27 conserved single copy orthologs in arthropods are missing from OGS2. Its genome also contains 2.1-fold more duplicated genes and 1.4-fold more single copy genes than the Drosophila melanogaster genome. The Nasonia gene count is larger than those of other sequenced hymenopteran species, owing both to improvements in the genome annotation and to unique genes in the wasp lineage. We identify 1008 genes and 171 gene families that deviate significantly from other hymenopterans in their rates of protein evolution and duplication history, respectively. We also provide an analysis of alternative splicing that reveals that genes with no annotated isoforms are characterized by shorter transcripts, fewer introns, faster protein evolution and higher probabilities of duplication than genes having alternative transcripts. Genome-wide expression data greatly improves the annotation of the N. vitripennis genome, by increasing the gene count, reducing the number of missing genes and providing more comprehensive data on splicing and gene structure. The improved gene set identifies lineage-specific genomic features tied to Nasonia's biology, as well as numerous novel genes. OGS2 and its associated search tools are available at http://arthropods.eugenes.org/EvidentialGene/nasonia/ , www.hymenopteragenome.org/nasonia/ and waspAtlas: www.tinyURL.com/waspAtlas . The EvidentialGene pipeline is available at https://sourceforge.net/projects/evidentialgene/ .

Twitter Demographics

The data shown below were collected from the profiles of 9 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 36 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 2 6%
Netherlands 1 3%
Unknown 33 92%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 12 33%
Researcher 9 25%
Student > Master 5 14%
Unspecified 3 8%
Other 2 6%
Other 5 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 20 56%
Biochemistry, Genetics and Molecular Biology 8 22%
Unspecified 4 11%
Computer Science 2 6%
Environmental Science 2 6%
Other 0 0%

Attention Score in Context

This research output has an Altmetric Attention Score of 4. 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 01 December 2016.
All research outputs
#1,960,878
of 8,711,471 outputs
Outputs from BMC Genomics
#1,481
of 6,079 outputs
Outputs of similar age
#74,254
of 255,599 outputs
Outputs of similar age from BMC Genomics
#65
of 275 outputs
Altmetric has tracked 8,711,471 research outputs across all sources so far. Compared to these this one has done well and is in the 76th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 6,079 research outputs from this source. They receive a mean Attention Score of 4.2. This one has gotten more attention than average, scoring higher than 74% of its peers.
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 255,599 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 70% of its contemporaries.
We're also able to compare this research output to 275 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 76% of its contemporaries.