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Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Overview of attention for article published in BMC Genomics, March 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 (86th percentile)
  • Good Attention Score compared to outputs of the same age and source (77th percentile)

Mentioned by

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27 tweeters
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1 Facebook page

Citations

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35 Dimensions

Readers on

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60 Mendeley
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Title
Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes
Published in
BMC Genomics, March 2017
DOI 10.1186/s12864-017-3654-1
Pubmed ID
Authors

Peng Zhou, Kevin A. T. Silverstein, Thiruvarangan Ramaraj, Joseph Guhlin, Roxanne Denny, Junqi Liu, Andrew D. Farmer, Kelly P. Steele, Robert M. Stupar, Jason R. Miller, Peter Tiffin, Joann Mudge, Nevin D. Young

Abstract

Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome. Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable - estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation. Analysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation.

Twitter Demographics

The data shown below were collected from the profiles of 27 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 60 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 60 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 19 32%
Student > Ph. D. Student 14 23%
Student > Bachelor 6 10%
Student > Master 6 10%
Other 5 8%
Other 9 15%
Unknown 1 2%
Readers by discipline Count As %
Agricultural and Biological Sciences 35 58%
Biochemistry, Genetics and Molecular Biology 11 18%
Computer Science 6 10%
Pharmacology, Toxicology and Pharmaceutical Science 2 3%
Unspecified 1 2%
Other 3 5%
Unknown 2 3%

Attention Score in Context

This research output has an Altmetric Attention Score of 15. 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 21 March 2019.
All research outputs
#1,222,567
of 14,612,915 outputs
Outputs from BMC Genomics
#450
of 8,505 outputs
Outputs of similar age
#35,680
of 262,764 outputs
Outputs of similar age from BMC Genomics
#5
of 22 outputs
Altmetric has tracked 14,612,915 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 91st percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 8,505 research outputs from this source. They receive a mean Attention Score of 4.2. This one has done particularly well, scoring higher than 94% 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 262,764 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 86% of its contemporaries.
We're also able to compare this research output to 22 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 77% of its contemporaries.