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The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

Overview of attention for article published in BMC Genomics, July 2015
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (84th percentile)
  • High Attention Score compared to outputs of the same age and source (90th percentile)

Mentioned by

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19 tweeters

Citations

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69 Dimensions

Readers on

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125 Mendeley
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Title
The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum
Published in
BMC Genomics, July 2015
DOI 10.1186/s12864-015-1756-1
Pubmed ID
Authors

Robert King, Martin Urban, Michael C. U. Hammond-Kosack, Keywan Hassani-Pak, Kim E. Hammond-Kosack

Abstract

Accurate genome assembly and gene model annotation are critical for comparative species and gene functional analyses. Here we present the completed genome sequence and annotation of the reference strain PH-1 of Fusarium graminearum, the causal agent of head scab disease of small grain cereals which threatens global food security. Completion was achieved by combining (a) the BROAD Sanger sequenced draft, with (b) the gene predictions from Munich Information Services for Protein Sequences (MIPS) v3.2, with (c) de novo whole-genome shotgun re-sequencing, (d) re-annotation of the gene models using RNA-seq evidence and Fgenesh, Snap, GeneMark and Augustus prediction algorithms, followed by (e) manual curation. We have comprehensively completed the genomic 36,563,796 bp sequence by replacing unknown bases, placing supercontigs within their correct loci, correcting assembly errors, and inserting new sequences which include for the first time complete AT rich sequences such as centromere sequences, subtelomeric regions and the telomeres. Each of the four F. graminearium chromosomes was found to be submetacentric with respect to centromere positioning. The position of a potential neocentromere was also defined. A preferentially higher frequency of genetic recombination was observed at the end of the longer arm of each chromosome. Within the genome 1529 gene models have been modified and 412 new gene models predicted, with a total gene call of 14,164. The re-annotation impacts upon 69 entries held within the Pathogen-Host Interactions database (PHI-base) which stores information on genes for which mutant phenotypes in pathogen-host interactions have been experimentally tested, of which 59 are putative transcription factors, 8 kinases, 1 ATP citrate lyase (ACL1), and 1 syntaxin-like SNARE gene (GzSYN1). Although the completed F. graminearum contains very few transposon sequences, a previously unrecognised and potentially active gypsy-type long-terminal-repeat (LTR) retrotransposon was identified. In addition, each of the sub-telomeres and centromeres contained either a LTR or MarCry-1_FO element. The full content of the proposed ancient chromosome fusion sites has also been revealed and investigated. Regions with high recombination previously noted to be rich in secretome encoding genes were also found to be rich in tRNA sequences. This study has identified 741 F. graminearum species specific genes and provides the first complete genome assembly for a Sordariomycetes species. This fully completed F. graminearum PH-1 genome and manually curated annotation, available at Ensembl Fungi, provides the optimum resource to perform interspecies comparative analyses and gene function studies.

Twitter Demographics

The data shown below were collected from the profiles of 19 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 125 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Netherlands 1 <1%
Brazil 1 <1%
Unknown 123 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 40 32%
Student > Master 25 20%
Researcher 24 19%
Student > Bachelor 11 9%
Student > Doctoral Student 8 6%
Other 12 10%
Unknown 5 4%
Readers by discipline Count As %
Agricultural and Biological Sciences 79 63%
Biochemistry, Genetics and Molecular Biology 22 18%
Computer Science 4 3%
Engineering 2 2%
Economics, Econometrics and Finance 2 2%
Other 6 5%
Unknown 10 8%

Attention Score in Context

This research output has an Altmetric Attention Score of 10. 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 24 March 2016.
All research outputs
#1,422,125
of 12,378,687 outputs
Outputs from BMC Genomics
#777
of 7,251 outputs
Outputs of similar age
#37,466
of 243,246 outputs
Outputs of similar age from BMC Genomics
#24
of 259 outputs
Altmetric has tracked 12,378,687 research outputs across all sources so far. Compared to these this one has done well and is in the 88th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 7,251 research outputs from this source. They receive a mean Attention Score of 4.3. This one has done well, scoring higher than 89% 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 243,246 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 84% of its contemporaries.
We're also able to compare this research output to 259 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 90% of its contemporaries.