Evidence map›Paper›PMID 34671909›Full record

ArticleVirus genes2022

Phylogenetics of tobacco rattle virus isolates from potato (Solanum tuberosum L.) in the USA: a multi-gene approach to evolutionary lineage.

Lindani Moyo, Gaurav Raikhy, Aflaq Hamid, Ipsita Mallik, Neil C Gudmestad, Stewart Gray, Hanu R Pappu

Abstract read
PubMed Publisher
In one paragraph

Article in Virus genes, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed, 1 pooled it
0.7field-weighted citation impact, top 22% of its field
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 synthesis or guideline pooled it, 4 citations in OpenAlex.

  1. Pooled it
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

7 authors at 4 institutions in 3 countries.

Lindani MoyoDepartment of Plant Pathology, Washington State University, Pullman, WA, 99164, USA.ORCID http://orcid.org/0000-0002-4196-9868
Gaurav RaikhyDepartment of Plant Pathology, Washington State University, Pullman, WA, 99164, USA.
Aflaq HamidDepartment of Plant Pathology, Washington State University, Pullman, WA, 99164, USA.
Ipsita MallikDepartment of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA.
Neil C GudmestadDepartment of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA.
Stewart GraySection of Plant Pathology and Plant-Microbe Biology, School of Plant Science, Cornell University, Ithaca, NY, 14853, USA.
Hanu R PappuDepartment of Plant Pathology, Washington State University, Pullman, WA, 99164, USA. hrp@wsu.edu.
Washington State University · USNorth Dakota State University · USCornell University · USStellenbosch University · ZA

Funding

usda national institute of food and agriculture Hatch project Accession #1016563 "Reducing the Impact of Pests and Diseases Affecting Washington Agriculture"usda-nifa-scri 2014-51181-22373
6 · The paper itself

Abstract

Tobacco rattle virus (TRV) is an important soil-borne virus of potato that is transmitted by stubby-root nematodes. TRV causes corky ringspot, a tuber disease of economic importance to potato production. Utilizing protein-coding regions of the whole genome and a range of computational tools, the genetic diversity, and population structure of TRV isolates from several potato-growing regions (Colorado, Idaho, Indiana, Minnesota, Nebraska, North Dakota, and Washington State) in the USA were determined. Phylogenetic analyses based on RNA2 nucleotide sequences, the coat protein (CP) and nematode transmission (2b) genes, showed geographical clustering of USA isolates with previously known American isolates, while European isolates grouped in a distinct cluster. This was corroborated by the observed genetic differentiation and infrequent gene flow between American and European isolates. Low genetic diversity was revealed among American isolates compared to European isolates. Phylogenetic clustering based on RNA1 genes (RdRp, RdRp-RT, and 1a) were all largely incongruent to that of 1b gene (virus suppressor of RNA silencing). This genetic incongruence suggested the influence of recombination. Furthermore, the RdRp, RdRp-RT, and 1a genes were predicted to be more conserved and under negative selection, while the 1b gene was less constrained. Different evolutionary lineages between TRV RNA1 and RNA2 genomic segments were revealed.

Indexed as

Plant VirusesSolanum tuberosumGenome, ViralNicotianaPhylogenyPlant DiseasesRNA, ViralRNA, ViralEvolutionGenetic diversityPotato virusRecombinationRNA virusTobacco rattle virusTobravirusVirgaviridae

Identifiers

PMID34671909
OpenAlexW3207752210

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.