Phylogenetic analysis of Tomato mosaic virus from Hemerocallis sp. and Impatiens hawkeri

Duarte, L. M. L.; Alexandre, M. A. V.; Rivas, Eliana Borges; Cattai, Marina Blanco; Soares, Rodrigo Martins; Harakava, Ricardo; Fernandes, Flora Maria de Campos

doi:10.1590/s0100-54052007000400016

Cited by 11 publications

(5 citation statements)

References 16 publications

(18 reference statements)

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“…Th e literature revealed the reports of potyvirus on amaryllis from India (Raj et al, 2009), tomato mosaic virus on H. fulva from Brazil (Duarte et al, 2007) and dasheen mosaic potyvirus on T. trilobatum from Vietnam (Ha et al, 2008). However, infection of CMV on A. calamus, D. pinnata, T. trilobatum and H. fulva has not been reported from any part of the world.…”

Section: Discussionmentioning

confidence: 99%

Sequence analysis and genetic diversity of five new Indian isolates of cucumber mosaic virus

Kumar¹,

Gautam²,

Raj³

2015

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Cucumber mosaic virus (CMV) is an important virus since it causes severe losses to many economically important crops worldwide. Five new isolates of CMV were isolated from naturally infected Hippeastrum hybridum, Dahlia pinnata, Hemerocallis fulva, Acorus calamus and Typhonium trilobatum plants, all exhibiting severe leaf mosaic symptoms. For molecular identifi cation and sequence analyses, the complete coat protein (CP) gene of these isolates was amplifi ed by RT-PCR. Th e resulting amplicons were cloned and sequenced and isolates were designated as HH (KP698590), DP (JF682239), HF (KP698589), AC (KP698588) and TT (JX570732). For study of genetic diversity among these isolates, the sequence data were analysed by BLASTn, multiple alignment and generating phylogenetic trees along with the respective sequences of other CMV isolates available in GenBank Database were done. Th e isolates under study showed 82-99% sequence diversity among them at nucleotide and amino acid levels; however they showed close relationships with CMV isolates of subgroup IB. In alignment analysis of amino acid sequences of HH and AC isolates, we have found fi ft een and twelve unique substitutions, compared to HF, DP and TT isolates, suggesting the cause of high genetic diversity.

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Section: Discussionmentioning

confidence: 99%

Sequence analysis and genetic diversity of five new Indian isolates of cucumber mosaic virus

Kumar¹,

Gautam²,

Raj³

2015

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“…Various phylogenetic analyses were conducted to better understand the genomic relationship of the ToBRFV and PepMV isolates in grocery store-purchased tomatoes and their origin of production sites. In the absence of a complete genome sequence, the phylogenetic study of tobamoviruses was often established using the complete CP sequence [42][43][44]. Our phylogenetic analysis, incorporating the complete CP gene sequence of ToBRFV isolates from this study and representative isolates from GenBank, revealed no noteworthy association between genomic diversity and geographical origins (e.g., Canada, Mexico, and the repacked U.S.).…”

Section: Discussionmentioning

confidence: 85%

Co-Infection of Tomato Brown Rugose Fruit Virus and Pepino Mosaic Virus in Grocery Tomatoes in South Florida: Prevalence and Genomic Diversity

Yilmaz,

Batuman

2023

Viruses

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Tomato brown rugose fruit virus (ToBRFV) is an economically important seed and mechanically transmitted pathogen of significant importance to tomato production around the globe. Synergistic interaction with pepino mosaic virus (PepMV), another seed and mechanically transmitted virus, and long-distance dissemination of these two viruses via contaminated tomato fruits through global marketing were previously suggested. In 2019, we detected both viruses in several grocery store-purchased tomatoes in South Florida, USA. In this study, to identify potential sources of inoculum, co-infection status, prevalence, and genomic diversity of these viruses, we surveyed symptomatic and asymptomatic imported tomatoes sold in ten different groceries in four cities in South Florida. According to the product labels, all collected tomatoes originated from Canada, Mexico, or repacking houses in the United States. With high prevalence levels, 86.5% of the collected samples were infected with ToBRFV, 90% with PepMV alone, and 73% were mixed-infected. The phylogenetic study showed no significant correlations between ToBRFV genomic diversity and the tomato label origin. Phylogenetic analysis of PepMV isolates revealed the prevalence of the PepMV strains, Chilean (CH2) and recombinant (US2). The results of this study highlight the continual presence of PepMV and ToBRFV in imported tomatoes in Florida grocery stores.

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“…When full genome sequence data were absent, the phylogenetic relationships among the isolates of tobamoviruses were often established using full CP sequences [ 38 , 39 , 40 ]. Therefore, the three groups of ToBRFV phylogeny, based on 480 bp full CP gene nt sequences, were confirmed in this study.…”

Section: Discussionmentioning

confidence: 99%

Insight into Population Structure and Evolutionary Analysis of the Emerging Tomato Brown Rugose Fruit Virus

Çeli̇k

Coşkan²,

Morca³

et al. 2022

Plants

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A total of 112 symptomatic tomatoes (Solanum lycopersicum L.) and 83 symptomatic pepper (Capsicum spp.) samples were collected in Ankara, Eskişehir, Bartın, and Zonguldak provinces of Turkey during 2020–2021. Six tomatoes and one pepper sample (3.6%) tested positive for tomato brown rugose fruit virus (ToBRFV, genus Tobamovirus) infection by DAS-ELISA and RT-PCR. ToBRFV-positive tomato and pepper plants were removed from greenhouses as soon as possible, and the greenhouses and tools were disinfected completely. Phylogenetic analysis on the complete CP sequences suggested the clustering of 178 GenBank isolates and 7 novel isolates into three groups. A study using DnaSP software showed very low genetic variation among current global ToBRFV isolates. All four ORFs of the virus genome were under strong negative evolutionary constraints, with a ω value range of 0.0869–0.2066. However, three neutrality tests indicated that most populations of the newly identified ToBRFV are currently expanding by assigning statistically significant negative values to them. The very low FST values (0.25 or less) obtained by all comparisons of the isolates from Europe, the Middle East, China, and America concluded that there is no clear genetic separation among currently known isolates from different geographic origins. The divergence time of ToBRFV was estimated to be in the middle of the course of the evolution of 11 tested tobamoviruses. The time to the most recent common ancestors (TMRCAs) of ToBRFV were calculated to be 0.8 and 1.87 with the genetically closest members of Tobamovirus. The results of this study could improve our understanding on the population structure of the emerging ToBRFV.

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Phylogenetic analysis of Tomato mosaic virus from Hemerocallis sp. and Impatiens hawkeri

Cited by 11 publications

References 16 publications

Sequence analysis and genetic diversity of five new Indian isolates of cucumber mosaic virus

Sequence analysis and genetic diversity of five new Indian isolates of cucumber mosaic virus

Co-Infection of Tomato Brown Rugose Fruit Virus and Pepino Mosaic Virus in Grocery Tomatoes in South Florida: Prevalence and Genomic Diversity

Insight into Population Structure and Evolutionary Analysis of the Emerging Tomato Brown Rugose Fruit Virus

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