Evidence map›Paper›PMID 41730992›Full record

ArticleScientific reports2026

Metatranscriptomics analysis reveals the cotton virome in the southern United States.

Cesar Escalante, Anyi M Reyes, Chaoyang Zhao, Kipling S Balkcom, Alana L Jacobson, Amanda Strayer-Scherer, Kathleen M Martin, Jenny Koebernick, Anders Huseth, Edmund Kozieł and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
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

18 authors.

Cesar EscalanteDepartment of Botany and Plant Pathology, Purdue University, West Lafayette, 47907, IN, USA. escalac@purdue.edu.
Anyi M ReyesDepartment of Entomology and Plant Pathology, Auburn University, Auburn, 36849, AL, USA.
Chaoyang ZhaoNational Soil Dynamics Laboratory, USDA-ARS, Auburn, 36849, AL, USA.
Kipling S BalkcomNational Soil Dynamics Laboratory, USDA-ARS, Auburn, 36849, AL, USA.
Alana L JacobsonDepartment of Entomology and Plant Pathology, Auburn University, Auburn, 36849, AL, USA.
Amanda Strayer-SchererDepartment of Entomology and Plant Pathology, Auburn University, Auburn, 36849, AL, USA.
Kathleen M MartinDepartment of Entomology and Plant Pathology, Auburn University, Auburn, 36849, AL, USA.
Jenny KoebernickDepartment of Crop, Soil and Environmental Sciences, Auburn University, Auburn, 36849, AL, USA.
Anders HusethDepartment of Entomology, Michigan State University, East Lansing, 48824, MI, USA.
Edmund KoziełInstitute of Biology, Department of Botany and Plant Physiology, Warsaw University of Life Sciences-SGGW, 159 Nowoursynowska Street, Warsaw, 02-776, Poland.
Ian SmallDepartment of Plant Pathology, University of Florida, Quincy, 32351, FL, USA.
Jeremy K GreeneDepartment of Plant and Environmental Sciences, Edisto Research and Education Center, Clemson University, Blackville, 29817, SC, USA.
Katarzyna Otulak-KoziełInstitute of Biology, Department of Botany and Plant Physiology, Warsaw University of Life Sciences-SGGW, 159 Nowoursynowska Street, Warsaw, 02-776, Poland.
Michael J MulvaneyDepartment of Plant and Soil Sciences, Mississippi State University, Mississippi State, 39762, MS, USA.
Paul P PriceDepartment of Plant Pathology and Crop Physiology, Macon Ridge Research Station, LSU AgCenter, Winnsboro, 71295, LA, USA.
Ricardo I Alcalá BriseñoDepartment of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, 16802, PA, USA.
Sudeep BagDepartment of Plant Pathology, University of Georgia, Tifton, 31794, GA, USA.
Kassie ConnerAlabama Cooperative Extension System, Auburn University, Auburn, 36849, AL, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

High-throughput sequencing (HTS) has expanded our perspective on the distribution and diversity of plant viruses. Furthermore, improvements in HTS and decreasing sample costs have enabled the discovery of novel plant viruses in field-collected samples. This study examined the putative virome of cotton samples collected from fields across the southern United States. Leaf samples were collected, and total RNA was extracted. Library preparation was performed from pooled samples within locations before sequencing on an Illumina platform. Sequenced libraries were mapped to the cotton reference genome, and the resulting sequences were de novo assembled. A metatranscriptomics analysis revealed complete genome contigs of cotton leafroll dwarf virus in all tested samples. Additionally, 29 putative families of RNA and DNA plant viruses co-infecting cotton were found. Seven families of RNA viruses were more prevalent across all locations. These families included Botourmiaviridae, Hypoviridae, Mitoviridae, Narnaviridae, Partitiviridae, Solemoviridae, and Totiviridae. The information obtained in this investigation will help develop a broader perspective on cotton virus diversity and whether co-infections of viruses can influence (negatively or positively) plant physiology, product quality, and yield.

Indexed as

GossypiumPlant VirusesTranscriptomeViromeGene Expression ProfilingGenome, ViralHigh-Throughput Nucleotide SequencingMetagenomicsPhylogenyRNA VirusesUnited States

Identifiers

PMID41730992
PMCPMC13031293

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Registered trials

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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.