Prevalence and phylogenetic analysis of Fig mosaic virus and Fig badnavirus-1 in Iran

Abstract Fig mosaic virus (FMV) and Fig badnavirus-1 (FBV-1) are two of the most important fig infecting viruses. The incidence and distribution of FBV-1 and FMV were determined by testing in PCR 138 asymptomatic and symptomatic samples. These samples were collected from 60 fig gardens and agricultural fields in three provinces of Iran. The fig infecting viruses FBV-1 and FMV, respectively, were detected in 92 (66.6%) and 34 (24.6%) samples collected from all the surveyed fields. Overall, 24 out of 138 (17.3%) samples showed mixed infections. The sequence analysis of a genomic fragment of 922 nt, comprising the entire ORF-2 and part of the 5’ termini of the ORF-3 of 10 selected FBV-1 Iranian isolates from different provinces, and of the type member from GenBank (Acc. No: JF411989), showed a variation ranging from 1 to 3% at nucleotide level and 1% at the amino acid level. The phylogenetic analysis grouped the FBV-1 isolates into two groups, with the Iranian isolates clustered in two distinct subgroups of group I, according to their geographical origin. In our research, the prevalence and sequence analysis of FBV-1 as the only identified DNA virus infecting fig trees, was studied for the first time in Iran.

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Genetic Variation and Possible Mechanisms Driving the Evolution of Worldwide Fig mosaic virus Isolates

Phytopathology ◽

10.1094/phyto-05-13-0145-r ◽

2014 ◽

Vol 104 (1) ◽

pp. 108-114 ◽

Cited By ~ 19

Author(s):

Jeewan Jyot Walia ◽

Anouk Willemsen ◽

Eminur Elci ◽

Kadriye Caglayan ◽

Bryce W. Falk ◽

...

Keyword(s):

Genetic Variation ◽

Mosaic Virus ◽

Rna Virus ◽

Plant Viruses ◽

Long Distance ◽

Evolutionary Mechanisms ◽

Plant Materials ◽

Genomic Rnas ◽

Fig Trees ◽

Fig Mosaic Virus

Fig mosaic virus (FMV) is a multipartite negative-sense RNA virus infecting fig trees worldwide. FMV is transmitted by vegetative propagation and grafting of plant materials, and by the eriophyid mite Aceria ficus. In this work, the genetic variation and evolutionary mechanisms shaping FMV populations were characterized. Nucleotide sequences from four genomic regions (each within the genomic RNAs 1, 2, 3, and 4) from FMV isolates from different countries were determined and analyzed. FMV genetic variation was low, as is seen for many other plant viruses. Phylogenetic analysis showed some geographically distant FMV isolates which clustered together, suggesting long-distance migration. The extent of migration was limited, although varied, between countries, such that FMV populations of different countries were genetically differentiated. Analysis using several recombination algorithms suggests that genomes of some FMV isolates originated by reassortment of genomic RNAs from different genetically similar isolates. Comparison between nonsynonymous and synonymous substitutions showed selection acting on some amino acids; however, most evolved neutrally. This and neutrality tests together with the limited gene flow suggest that genetic drift plays an important role in shaping FMV populations.

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Biological and Molecular Diversity of Cucumber green mottle mosaic virus in Spain

Plant Disease ◽

10.1094/pdis-09-16-1220-re ◽

2017 ◽

Vol 101 (6) ◽

pp. 977-984 ◽

Cited By ~ 7

Author(s):

Oscar Crespo ◽

Dirk Janssen ◽

Carmen García ◽

Leticia Ruiz

Keyword(s):

Mosaic Virus ◽

Molecular Diversity ◽

Geographical Origin ◽

Enzyme Analysis ◽

Restriction Enzyme Analysis ◽

Rt Pcr ◽

Chenopodium Amaranticolor ◽

First Time ◽

Partial Genome ◽

Range Study

The complete RNA genome from Cucumber green mottle mosaic virus (CGMMV) (Alm08), collected during 2009 in cucumber crops located in Spain, was found to be 6,422 nucleotides long. The nucleotide sequence shared the highest identity with isolates from Russia (GQ495274, GQ495275, FJ848666) as do nucleotide sequences of partial CP and MP genes described in Spain since 2005. All the partial genome sequences including RdRp, CP, and MP from 26 isolates collected from 2013 to 2015 in the southeast of Spain, and from seven isolates of other parts of the world, suggest that they grouped in two major clusters: one cluster (I) included 14 isolates collected between 2013 and 2014, and also reference isolates from France, the Netherlands, and Uzbekistan. A second cluster (II) grouped 12 isolates, which were mostly collected in 2015 together with those from Japan, South Korea, and Canada. For the first time, CGMMV isolates of different geographical origin were found coinfecting the same crop and territory. A host range study revealed that representative isolates of cluster II, but not from cluster I, produced local lesions in Chenopodium amaranticolor. RT-PCR using a common primer pair for CGMMV followed by restriction enzyme analysis with KpnI allowed distinguishing cluster I from II CGMMV isolates.

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(257) Pepino Mosaic Virus: Variability in U.S. Isolates

HortScience ◽

10.21273/hortsci.40.4.1089b ◽

2005 ◽

Vol 40 (4) ◽

pp. 1089B-1089

Author(s):

Clarissa J. Maroon-Lango ◽

Mary Ann Guaragna ◽

Ramon Jordan ◽

John Hammond ◽

Murali Bandla ◽

...

Keyword(s):

United States ◽

Mosaic Virus ◽

Amino Acid Level ◽

The United States ◽

Full Length ◽

Nucleotide Level ◽

Tomato Fruits ◽

Pepino Mosaic Virus ◽

Infected Tomato ◽

Germplasm Accessions

Pepino mosaic virus (PepMV) was first found in pepino (Solanum muricatum) growing in coastal Peru in 1974 and described in 1980; it reappeared in protected tomato (Lycopersiconesculentum) in the Netherlands in 1999. Since then, it has been reported to occur in tomato in several countries including Austria, Belgium, Canada, France, Germany, Italy, Peru, Spain and the Canary Islands, the United Kingdom, and in 11 states within the United States. Three strains of PepMV found in the United States have been cloned and sequenced. Full-length genomic sequences were obtained for two strains, PepMV-US1 and PepMV-US2, from co-infected tomato plant samples from Arizona. The 3'-end sequence of PepMV-US3 came from infected tomato fruits from Maryland. The genome organization, motifs and domains typical of the genus Potexvirus, and of other PepMV isolates, were found in full-length sequences of both US1 and US2 isolates. Direct comparison of US1 and US2 at the nucleotide level revealed an 86.3% identity; whereas, when individually compared to the French and Spanish isolates, which share ∼99% identity at the nucleotide level, US1 and US2 had 82% and 79% identities to each, respectively. Pair-wise gene-for-gene comparisons between United States and European isolates revealed a similar trend. While unique, US1 is more closely related to the previously reported European isolates than is US2. The CP of US3 is nearly identical to the European isolates at the amino acid level. None of 18 tomato germplasm accessions or 10 cultivars were resistant to mechanical inoculation with US3; in contrast, no infection was detected in nine pepper cultivars or four germplasm accessions. Plants grown from seeds of infected tomato fruits did not test positive for PepMV.

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Phylogenetic Analysis and Molecular Typing of Trichothecene-Producing Fusarium Fungi from Russian Collections

Acta Naturae ◽

10.32607/20758251-2018-10-2-79-92 ◽

2018 ◽

Vol 10 (2) ◽

pp. 79-92

Author(s):

A. A. Stakheev ◽

L. V. Samokhvalova ◽

O. D. Mikityuk ◽

S. K. Zavriev

Keyword(s):

Phylogenetic Analysis ◽

Fusarium Species ◽

Geographic Origin ◽

Elongation Factor ◽

Intraspecific Variability ◽

North Caucasus ◽

The North ◽

Group I ◽

High Level ◽

First Time

We performed a three-locus phylogenetic analysis of Fusarium strains presumably capable of trichothecene production, which were deposited in the Russian national collections. The intra- and interspecific polymorphism of partial sequences of the translation elongation factor 1 alpha (TEF1) gene and two genes from the trichothecene cluster TRI5 and TRI14 was studied. A study of 60 strains of different origins using DNA markers confirmed, and in the case for several strains, clarified their taxonomic characteristics. As a result, a strain of F. commune (F-900) was identified in Russia for the first time. Furthermore, the strain F-846 proved to be phylogenetically distinct from any of the known Fusarium species. F. equiseti strains from Northwest Russia were found to belong to the North European group (I), whereas a strain from the North Caucasus - to the South European one (II). Partial TRI14 sequences from 9 out of 12 species were determined for the first time. Their comparative analysis demonstrated a relatively high level of intraspecific variability in F. graminearum and F. sporotrichioides, but no correlation between the sequence polymorphism and the geographic origin of the strains or their chemotype was found. Specific chemotypes of trichothecene B producers were characterized using two primer sets. The chemotyping results were verified by HPLC.

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Prevalence and molecular characteristics of rotaviruses from Polish turkey flocks between 2008 and 2011

Bulletin of the Veterinary Institute in Pulawy ◽

10.2478/bvip-2013-0080 ◽

2013 ◽

Vol 57 (4) ◽

pp. 461-465 ◽

Cited By ~ 1

Author(s):

Katarzyna Domańska-Blicharz ◽

Anna Jacukowicz ◽

Zenon Minta

Keyword(s):

Phylogenetic Analysis ◽

Sequence Analysis ◽

Geographical Origin ◽

Molecular Characteristics ◽

Nsp4 Gene ◽

Group Affiliation ◽

Pcr Assay ◽

Distinct Subgroup ◽

Commercial Turkey ◽

European Group

Abstract Between 2008 and 2011, commercial turkey flocks in Poland were examined for the presence of rotaviruses. Ten faecal swabs from each of 207 turkey flocks (turkeys aged one to 19 weeks) were collected in different regions of the country and tested using a PCR assay that targeted the NSP4 gene. The prevalence of rotavirus was 20.3% in the flocks tested. Phylogenetic analysis revealed a clear division into groups dependent on geographical origin of the analysed viruses. All Polish rotaviruses belonged to the European group. However, they were found to be genetically variable based on the sequence analysis. The most frequently identified rotaviruses belonged to RV-1 subgroup and two of them formed a distinct subgroup of RV-2. Rotaviruses were detected in healthy and enteric turkeys. The observed amino acid changes probably did not affect the group affiliation, nor the pathogenecity of the studied rotavirus strains.

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Comparison by Sequence-Based and Electron Microscopic Analyses of Fig mosaic virus Isolates Obtained from Field and Experimentally Inoculated Fig Plants

Plant Disease ◽

10.1094/pdis-11-09-0771 ◽

2010 ◽

Vol 94 (12) ◽

pp. 1448-1452 ◽

Cited By ~ 6

Author(s):

Kadriye Çağlayan ◽

Çiğdem Ulubaş Serçe ◽

Eminur Barutçu ◽

Kamuran Kaya ◽

Vicente Medina ◽

...

Keyword(s):

Electron Microscopy ◽

Mosaic Virus ◽

Mosaic Disease ◽

Electron Microscopic ◽

Mesophyll Cells ◽

Donor Plant ◽

Transmission Electron ◽

Pcr Products ◽

Fig Trees ◽

Fig Mosaic Virus

Fig mosaic disease (FMD) and the fig mite, Aceria ficus, are widespread in different fig growing provinces of Turkey. Fig trees (Ficus carica) cv. Bursa siyahı (D1) and an unknown seedling (D2) that showed typical FMD symptoms and was heavily infested by fig mites were used as donor plants for attempted mite transmissions to healthy fig seedlings. Transmission electron microscopy observations of donor plant samples prior to the transmission tests were performed and showed the presence of double membrane bodies (DMBs) in the palisade mesophyll cells. Electron microscopy of all experimentally inoculated fig seedlings showed the same bodies. This result reinforced the suggestion that an agent that elicits the production of DMBs in infected cells is involved in the etiology of FMD. Double-stranded (ds)RNA analyses were also performed from experimentally inoculated plants, and dsRNAs with sizes approximately 1.30 and 1.96 kb were obtained. Reverse transcription–polymerase chain reaction (RT-PCR) products of 468 and 298 bp specific to Fig mosaic virus (FMV) were amplified from both donor and experimentally inoculated plants. BLAST analyses of nucleotide sequences of these fragments showed 90% identity with FMV for the donor plant and 94 to 96% for experimentally inoculated plants. According to these results, FMV is present in both donor and experimentally inoculated plants in Turkey, and this virus is transmissible by A. ficus from fig plant to fig plant.

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First Report of a Novel Potyvirus from Florida Causing Chlorotic Mottling in Squash (Cucurbita pepo)

Plant Disease ◽

10.1094/pdis-01-13-0099-pdn ◽

2013 ◽

Vol 97 (9) ◽

pp. 1259-1259 ◽

Cited By ~ 2

Author(s):

O. A. Abdalla ◽

A. Ali

Keyword(s):

Mosaic Virus ◽

Consensus Sequence ◽

Amino Acid Level ◽

The United States ◽

Yellow Mosaic Virus ◽

Post Inoculation ◽

Rt Pcr ◽

Nucleotide Level ◽

Pcr Product ◽

Sds Page

During the 2010 to 2011 growing seasons, nine cucurbit leaf samples including cantaloupe, cucumber, pumpkin, squash, and watermelon, showing mosaic and mottling, were collected from fields in the Homestead and Tampa areas in Florida (1). Eight of the nine samples were positive by dot-immunobinding assay (DIBA) and reverse transcription (RT)-PCR for either Watermelon mosaic virus (WMV), Papaya ringspot virus (PRSV-W), or mixed infection of both viruses. One squash sample from the Homestead area showing unique symptoms including chlorotic spots, yellowing, mottling, vein clearing, and mild mosaic was negative by RT-PCR against PRSV-W, Squash vein yellowing virus (SqVYV), WMV, and Zucchini yellow mosaic virus (ZYMV).The presence of virus-like particles (VLP) from symptomatic squash leaves (1) was prepared as described previously (2). Typical potyvirus-like particles ~700 nm long and 12 to 14 nm wide were observed by electron microscope from VLP preparations. Analysis of VLP on SDS-PAGE demonstrated a slightly larger coat protein (CP) (37 kDa compared with PRSV-W [35 kDa]). Sap from symptomatic squash leaf samples or VLP was mechanically inoculated to 10 squash seedlings at cotyledon stage using 0.1 M K2HPO4 buffer. Chlorotic spots were observed on the first true leaf 7 days post inoculation. However, symptoms became more severe by 2 to 3 weeks post inoculation and systemically infected leaves showed chlorosis and mottling similar to the original symptoms when tissues were collected from the field. Mock-inoculated control squash seedlings did not produce any symptoms. Symptomatic leaves from mechanically infected squash plants were used for VLP preparations and virus particles and size of the CP on SDS-PAGE was observed as before. Total RNA was extracted from VLP (2) and tested by RT-PCR using universal Potyviridae primers (forward primer 5′-CACGGATCCCGGG (T)17AGC and reverse primer 5′-GGBAAYAAYAGYGGDCARCC (3) to amplify a fragment from the 3′ end of the genome (including part of NIb gene, whole CP). A band of 1.2 kb was observed when the PCR product was analyzed on 1% agarose gel. PCR product was purified using QIAquick PCR Purification Kit (QIAGEN, USA), cloned (pGEM-T Easy Vector, Promega, USA), and sequenced in both directions. Consensus sequence was obtained from at least five clones and submitted to GenBank (KC522968). A BLASTn comparing the sequence from the squash potyvirus to others in GenBank found the highest similarity was 72.0% at nucleotide level and 64.8% at amino acid level with PRSV-W (JN831646), and less than 70% nucleotide similarity with WMV (NC_006262) and SqVYV (NC_010521). Based on the particle morphology, CP size on SDS-PAGE, nucleotide identity with other cucurbit potyviruses, and unique symptoms, it is concluded that this could be a new potyvirus. The threshold for classifying distinct species in Potyviridae is less than 76% identity at nucleotide level for either CP gene or the whole genome (4). This virus has been tentatively named as Squash chlorosis mottling virus (SqCMV). Florida is one of the leading states in acreage and production of cucurbits in the United States. The emergence of this new virus could be a potential future threat to cucurbits production. References: (1) A. Ali et al. Plant Health Progress. Online publication. doi:10.1094/PHP-2012-0824-01-RS, 2012. (2) A. Ali et al. Plant Dis. 96:243, 2012. (3) A. Gibbs and A. Mackenzie. J. Virol. Methods 63:9, 1997. (4) A. M. Q. King et al. Virus Taxonomy-ICTV 9th Report:1071, 2012.

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Phylogenetic analysis of partial sequences from Fig mosaic virus isolates in Turkey

Phytoparasitica ◽

10.1007/s12600-013-0286-0 ◽

2013 ◽

Vol 41 (3) ◽

pp. 263-270 ◽

Cited By ~ 1

Author(s):

Eminur Elçi ◽

Çiğdem Ulubaş Serçe ◽

Kadriye Çağlayan

Keyword(s):

Phylogenetic Analysis ◽

Mosaic Virus ◽

Fig Mosaic Virus ◽

Virus Isolates

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New and noteworthy lichen-forming and lichenicolous fungi 10

Acta Botanica Hungarica ◽

10.1556/034.62.2020.1-2.6 ◽

2020 ◽

Vol 62 (1-2) ◽

pp. 69-108

Author(s):

S. Y. Kondratyuk ◽

D. K. Upreti ◽

G. K. Mishra ◽

S. Nayaka ◽

K. K. Ingle ◽

...

Keyword(s):

Phylogenetic Analysis ◽

South Korea ◽

Eastern Europe ◽

South Asia ◽

New Combinations ◽

Eastern Asia ◽

Forest Zone ◽

Mediterranean Europe ◽

First Time ◽

India And China

Eight species, new for science, i.e.: Lobothallia gangwondoana S. Y. Kondr., J.-J. Woo et J.-S. Hur and Phyllopsora dodongensis S. Y. Kondr. et J.-S. Hur from South Korea, Eastern Asia, Ioplaca rinodinoides S. Y. Kondr., K. K. Ingle, D. K. Upreti et S. Nayaka, Letrouitia assamana S. Y. Kondr., G. K. Mishra et D. K. Upreti, and Rusavskia indochinensis S. Y. Kondr., D. K. Upreti et S. Nayaka from India and China, South Asia, Caloplaca orloviana S. Y. Kondr. and Rusavskia drevlyanica S. Y. Kondr. et O. O. Orlov from Ukraine, Eastern Europe, as well as Xanthoria ibizaensis S. Y. Kondr. et A. S. Kondr. from Ibiza Island, Spain, Mediterranean Europe, are described, illustrated and compared with closely related taxa. Fominiella tenerifensis S. Y. Kondr., Kärnefelt, A. Thell et Feuerer is for the first time recorded from Mediterranean Europe, Huriella loekoesiana S. Y. Kondr. et Upreti is provided from Russia for the first time, and H. pohangensis S. Y. Kondr., L. Lőkös et J.-S. Hur for the first time from China, Phoma candelariellae Z. Kocakaya et Halıcı is new to Ukraine, and Staurothele frustulenta Vain. is recorded from the Forest Zone of Ukraine for the first time. Twelve new combinations, i.e.: Bryostigma apotheciorum (for Sphaeria apotheciorum A. Massal.), Bryostigma biatoricola (for Arthonia biatoricola Ihlen et Owe-Larss.), Bryostigma dokdoense (for Arthonia dokdoensis S. Y. Kondr., L. Lőkös, B. G. Lee, J.-J. Woo et J.-S. Hur), Bryostigma epiphyscium (for Arthonia epiphyscia Nyl.), Bryostigma lobariellae (for Arthonia lobariellae Etayo), Bryostigma lapidicola (for Lecidea lapidicola Taylor), Bryostigma molendoi (for Tichothecium molendoi Heufl. ex Arnold), Bryostigma neglectulum (for Arthonia neglectula Nyl.), Bryostigma parietinarium (for Arthonia parietinaria Hafellner et Fleischhacker), Bryostigma peltigerinum (for Arthonia vagans var. peltigerina Almq.), Bryostigma phaeophysciae (for Arthonia phaeophysciae Grube et Matzer), Bryostigma stereocaulinum (for Arthonia nephromiaria var. stereocaulina Ohlert), are proposed based on results of combined phylogenetic analysis based on mtSSU and RPB2 gene sequences. Thirty-one new combinations for members of the genus Polyozosia (i.e.: Polyozosia actophila (for Lecanora actophila Wedd.), Polyozosia agardhiana (for Lecanora agardhiana Ach.), Polyozosia altunica (for Myriolecis altunica R. Mamut et A. Abbas), Polyozosia antiqua (for Lecanora antiqua J. R. Laundon), Polyozosia bandolensis (for Lecanora bandolensis B. de Lesd.), Polyozosia behringii (for Lecanora behringii Nyl.), Polyozosia caesioalutacea (for Lecanora caesioalutacea H. Magn.), Polyozosia carlottiana (for Lecanora carlottiana C. J. Lewis et Śliwa), Polyozosia congesta (for Lecanora congesta Clauzade et Vězda), Polyozosia eurycarpa (for Lecanora eurycarpa Poelt, Leuckert et Cl. Roux), Polyozosia expectans (Lecanora expectans Darb.), Polyozosia flowersiana (Lecanora flowersiana H. Magn.), Polyozosia fugiens (for Lecanora fugiens Nyl.), Polyozosia invadens (for Lecanora invadens H. Magn.), Polyozosia juniperina (for Lecanora juniperina Śliwa), Polyozosia latzelii (for Lecanora latzelii Zahlbr.), Polyozosia liguriensis (for Lecanora liguriensis B. de Lesd.), Polyozosia massei (for Myriolecis massei M. Bertrand et J.-Y. Monnat), Polyozosia mons-nivis (for Lecanora mons-nivis Darb.), Polyozosia oyensis (for Lecanora oyensis M.-P. Bertrand et Cl. Roux), Polyozosia percrenata (for Lecanora percrenata H. Magn.), Polyozosia persimilis (for Lecanora hagenii subsp. persimilis Th. Fr.), Polyozosia poeltiana (for Lecanora poeltiana Clauzade et Cl. Roux), Polyozosia prominens (for Lecanora prominens Clauzade et Vězda), Polyozosia prophetae-eliae (for Lecanora prophetae-eliae Sipman), Polyozosia salina (for Lecanora salina H. Magn.), Polyozosia schofieldii (for Lecanora schofieldii Brodo), Polyozosia sverdrupiana (for Lecanora sverdrupiana Øvstedal), Polyozosia torrida (for Lecanora torrida Vain.), Polyozosia wetmorei (for Lecanora wetmorei Śliwa), Polyozosia zosterae (for Lecanora subfusca? zosterae Ach.)) are proposed.

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