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De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust

Overview of attention for article published in mBio, February 2018
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  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (96th percentile)
  • High Attention Score compared to outputs of the same age and source (92nd percentile)

Mentioned by

news
6 news outlets
blogs
1 blog
twitter
51 X users

Citations

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59 Dimensions

Readers on

mendeley
68 Mendeley
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Title
De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust
Published in
mBio, February 2018
DOI 10.1128/mbio.01650-17
Pubmed ID
Authors

Marisa E. Miller, Ying Zhang, Vahid Omidvar, Jana Sperschneider, Benjamin Schwessinger, Castle Raley, Jonathan M. Palmer, Diana Garnica, Narayana Upadhyaya, John Rathjen, Jennifer M. Taylor, Robert F. Park, Peter N. Dodds, Cory D. Hirsch, Shahryar F. Kianian, Melania Figueroa

Abstract

Oat crown rust, caused by the fungusPucinnia coronataf. sp.avenae, is a devastating disease that impacts worldwide oat production. For much of its life cycle,P. coronataf. sp.avenaeis dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguousde novogenome assemblies of twoP. coronataf. sp.avenaeisolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp; approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms inP. coronataf. sp.avenaeIMPORTANCEDisease management strategies for oat crown rust are challenged by the rapid evolution ofPuccinia coronataf. sp.avenae, which renders resistance genes in oat varieties ineffective. Despite the economic importance of understandingP. coronataf. sp.avenae, resources to study the molecular mechanisms underpinning pathogenicity and the emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle ofP. coronataf. sp.avenaeas well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic diversity in populations ofP. coronataf. sp.avenae.

X Demographics

X Demographics

The data shown below were collected from the profiles of 51 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 68 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 68 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 16 24%
Researcher 13 19%
Student > Bachelor 6 9%
Student > Master 4 6%
Professor 4 6%
Other 9 13%
Unknown 16 24%
Readers by discipline Count As %
Agricultural and Biological Sciences 29 43%
Biochemistry, Genetics and Molecular Biology 14 21%
Environmental Science 3 4%
Computer Science 2 3%
Arts and Humanities 1 1%
Other 2 3%
Unknown 17 25%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 80. 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 18 July 2019.
All research outputs
#539,175
of 25,563,770 outputs
Outputs from mBio
#402
of 6,560 outputs
Outputs of similar age
#12,395
of 344,835 outputs
Outputs of similar age from mBio
#12
of 151 outputs
Altmetric has tracked 25,563,770 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 97th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 6,560 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 24.9. This one has done particularly well, scoring higher than 93% 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 344,835 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 96% of its contemporaries.
We're also able to compare this research output to 151 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 92% of its contemporaries.