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An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

Overview of attention for article published in BMC Genomics, January 2017
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (90th percentile)
  • High Attention Score compared to outputs of the same age and source (91st percentile)

Mentioned by

blogs
1 blog
twitter
20 tweeters
facebook
1 Facebook page

Citations

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56 Dimensions

Readers on

mendeley
84 Mendeley
citeulike
1 CiteULike
Title
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod
Published in
BMC Genomics, January 2017
DOI 10.1186/s12864-016-3448-x
Pubmed ID
Authors

Ole K. Tørresen, Bastiaan Star, Sissel Jentoft, William B. Reinar, Harald Grove, Jason R. Miller, Brian P. Walenz, James Knight, Jenny M. Ekholm, Paul Peluso, Rolf B. Edvardsen, Ave Tooming-Klunderud, Morten Skage, Sigbjørn Lien, Kjetill S. Jakobsen, Alexander J. Nederbragt

Abstract

The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies. By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21% of the TRs across the assembly, 19% in the promoter regions and 12% in the coding sequences are heterozygous in the sequenced individual. The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 84 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 1%
Czechia 1 1%
Sweden 1 1%
Canada 1 1%
New Zealand 1 1%
Unknown 79 94%

Demographic breakdown

Readers by professional status Count As %
Researcher 22 26%
Student > Ph. D. Student 20 24%
Student > Master 10 12%
Unspecified 9 11%
Student > Doctoral Student 8 10%
Other 15 18%
Readers by discipline Count As %
Agricultural and Biological Sciences 47 56%
Biochemistry, Genetics and Molecular Biology 19 23%
Unspecified 12 14%
Computer Science 3 4%
Veterinary Science and Veterinary Medicine 1 1%
Other 2 2%

Attention Score in Context

This research output has an Altmetric Attention Score of 18. 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 20 December 2017.
All research outputs
#746,946
of 12,330,736 outputs
Outputs from BMC Genomics
#271
of 7,222 outputs
Outputs of similar age
#32,439
of 332,403 outputs
Outputs of similar age from BMC Genomics
#14
of 164 outputs
Altmetric has tracked 12,330,736 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 93rd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 7,222 research outputs from this source. They receive a mean Attention Score of 4.3. This one has done particularly well, scoring higher than 96% 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 332,403 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 90% of its contemporaries.
We're also able to compare this research output to 164 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 91% of its contemporaries.