Evidence map›Paper›PMID 38191299›Full record

ArticleBMC genomics2024

Insights into the genetic variability and evolutionary dynamics of tomato spotted wilt orthotospovirus in China.

Ali Kamran, Ying Li, Wanhong Zhang, Yubin Jiao, Tahir Farooq, Yong Wang, Dongyang Liu, Lianqiang Jiang, Lili Shen, Fenglong Wang and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2024. 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
  2. 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

11 authors.

Ali Kamran *Key Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China.
Ying Li *Key Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China.
Wanhong ZhangKey Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China.
Yubin JiaoKey Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China.
Tahir FarooqGuangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China.
Yong WangTobacco Company of Yunnan Province, Liangshan Company, 615000, Xichang, Sichuan, China.
Dongyang LiuTobacco Company of Yunnan Province, Liangshan Company, 615000, Xichang, Sichuan, China.
Lianqiang JiangTobacco Company of Yunnan Province, Liangshan Company, 615000, Xichang, Sichuan, China.
Lili ShenKey Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China.
Fenglong WangKey Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China. wangfenglong@caas.cn.ORCID http://orcid.org/0000-0002-3651-9395
Jinguang YangKey Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China. yangjinguang@caas.cn.

Funding

China National Tobacco Corporation 110202001033(LS-02),110202101045(LS-05),110202101027(LS-02)Natural Science Foundation of Shandong Province ZR202103070049
6 · The paper itself

Abstract

backgroundViral diseases are posing threat to annual production and quality of tobacco in China. Recently, tomato spotted wilt orthotospovirus (TSWV) has been reported to infect three major crops including tobacco. Current study was aimed to investigate the population dynamics and molecular diversity of the TSWV. In the current study, to assess and identify the prevalence and evolutionary history of TSWV in tobacco crops in China, full-length genome sequences of TSWV isolates from tobacco, were identified and analyzed.

methodsAfter trimming and validation, sequences of new isolates were submitted to GenBank. We identified the full-length genomes of ten TSWV isolates, infecting tobacco plants from various regions of China. Besides these, six isolates were partially sequenced. Phylogenetic analysis was performed to assess the relativeness of newly identified sequences and corresponding sequences from GenBank. Recombination and population dynamics analysis was performed using RDP4, RAT, and statistical estimation. Reassortment analysis was performed using MegaX software.

resultsPhylogenetic analysis of 41 newly identified sequences, depicted that the majority of the Chinese isolates have separate placement in the tree. RDP4 software predicted that RNA M of newly reported isolate YNKM-2 had a recombinant region spanning from 3111 to 3811 bp. The indication of parental sequences (YNKMXD and YNHHKY) from newly identified isolates, revealed the conservation of local TSWV population. Genetic diversity and population dynamics analysis also support the same trend. RNA M was highlighted to be more capable of mutating or evolving as revealed by data obtained from RDP4, RAT, population dynamics, and phylogenetic analyses. Reassortment analysis revealed that it might have happened in L segment of TSWV isolate YNKMXD (reported herein).

conclusionTaken together, this is the first detailed study revealing the pattern of TWSV genetic diversity, and population dynamics helping to better understand the ability of this pathogen to drastically reduce the tobacco production in China. Also, this is a valuable addition to the existing worldwide profile of TSWV, especially in China, where a few studies related to TSWV have been reported including only one complete genome of this virus isolated from tobacco plants.

Indexed as

RNA VirusesSolanum lycopersicumBiological EvolutionChinaCrops, AgriculturalNicotianaPhylogenyRNARNAGenetic diversityPhylogenetic analysisPopulation dynamics, statistical estimationReassortmentRecombinationTomato spotted wilt orthotospovirus

Identifiers

PMID38191299
PMCPMC10773106

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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.