Evidence map›Paper›PMID 40251471›Full record

ArticleBMC genomics2025

The first chromosome-scale genome assembly of a microcyclic rust, Puccinia silphii.

Jacqueline S de Mattos, Kyle Keepers, Peter A Innes, Clifton P Bueno de Mesquita, C Alisha Quandt, Nolan C Kane, Yaniv Brandvain, Kathryn Turner

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PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Jacqueline S de MattosDepartment of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street, Boulder, CO, 80309-0334, USA.
Kyle KeepersDepartment of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street, Boulder, CO, 80309-0334, USA. kylekeepers@gmail.com.
Peter A InnesDepartment of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street, Boulder, CO, 80309-0334, USA.
Clifton P Bueno de MesquitaDepartment of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street, Boulder, CO, 80309-0334, USA.
C Alisha QuandtDepartment of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street, Boulder, CO, 80309-0334, USA.
Nolan C KaneDepartment of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street, Boulder, CO, 80309-0334, USA.
Yaniv BrandvainDepartment of Plant and Microbial Biology, University of Minnesota, 1500 Gortner Ave, St Paul, MN, 55108, USA.
Kathryn TurnerCrop Protection Ecology, The Land Institute, 2440 E Water Well Rd, Salina, KS, 67401, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundRust fungi are destructive pathogens in crop plants, having led to epidemics and damaging crops all over the world. The rust Puccinia silphii (Basidiomycota) infects Silphium integrifolium, which is a member of the most speciose plant family, Asteraceae.

resultsThis study analyzes the first chromosome-scale genome sequence of a rust that infects any dicot, or any species outside of the Poaceae (grasses). We found it to be the smallest genome among the available Pucciniales genome assemblies. Our final assembly was 41.7 Mb in size and consisted of 19 pseudomolecules. The genome had a BUSCO completeness score of 92.1%, with nearly all BUSCO gene losses shared with other Puccinia genomes, and gene losses concentrated in the sulfate assimilation categories. Other gene losses were unique to P. silphii, whose genome contained by far the fewest protein coding genes. A total of 10,399 protein coding genes were predicted, compared to 14,257 in the next smallest genome. Gene losses in P. silphii were concentrated in categories related to meiosis.

conclusionThis newly assembled genome provides insights into the size limitations of Puccinia genus genomes, as well as important protein gene families that are evolving within the genus including sulphate assimilation genes and DNA replication and its role in the evolution of microcyclic rusts.

Indexed as

BasidiomycotaChromosomes, FungalGenome, FungalGenomicsPucciniaPlant DiseasesCrop genomicsCrop protection ecologyGenome assemblyPrairiesPucciniaRust diseaseRust fungi

Identifiers

PMID40251471
PMCPMC12007239

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.