Genetic variability and recombination analysis of papaya infecting isolates of Papaya ringspot virus based on CP gene from Western India

Local varieties of papaya grown in the Andean foothills of Mérida, Venezuela, were transformed independently with the coat protein (CP) gene from two different geographical Papaya ringspot virus (PRSV) isolates, designated VE and LA, via Agrobacterium tumefaciens. The CP genes of both PRSV isolates show 92 and 96% nucleotide and amino acid sequence similarity, respectively. Four PRSV-resistant R0 plants were intercrossed or selfed, and the progenies were tested for resistance against the homologous isolates VE and LA, and the heterologous isolates HA (Hawaii) and TH (Thailand) in greenhouse conditions. Resistance was affected by sequence similarity between the transgenes and the challenge viruses: resistance values were higher for plants challenged with the homologous isolates (92 to 100% similarity) than with the Hawaiian (94% similarity) and, lastly, Thailand isolates (88 to 89% similarity). Our results show that PRSV CP gene effectively protects local varieties of papaya against homologous and heterologous isolates of PRSV.

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Comparação da seqüência de nucleotídeos do gene da proteína capsidial de estirpes severas e premunizantes do Papaya ringspot virus

Fitopatologia Brasileira ◽

10.1590/s0100-41582003000600015 ◽

2003 ◽

Vol 28 (6) ◽

pp. 678-681 ◽

Cited By ~ 3

Author(s):

Marilia G. S. Della Vecchia ◽

Luis E. A. Camargo ◽

Jorge A. M. Rezende

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Core Region ◽

Amino Acid Sequences ◽

Ringspot Virus ◽

Papaya Ringspot Virus ◽

Specific Primers ◽

Sequence Comparisons ◽

The Core ◽

Cp Gene

This study compared three mild and three severe strains of Papaya ringspot virus - type W (PRSV-W), based on nucleotide and amino acid sequences of the capsid protein (CP) gene. The CP nucleotide sequences of the mild strains shared 98% to 100% identity. When compared to the severe strains the identity ranged from 93% to 95%, except in the case of PRSV-W-2R, which resulted from reversion of the mild strains PRSV-W-2. The CP sequence of the reverting strain showed 100% identity with the sequence of its parental strain. An insertion of six nucleotides in the core region of the CP gene, which reflected the addition of two amino acids (Asn and Asp) in the deduced sequence of the protein, was found in all mild strains. These sequence comparisons were used to design strain-specific primers that were used to specifically amplify regions for either the mild or severe strains.

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Genetic variability of Papaya ringspot virus isolates in Norte de Santander - Colombia

Agronomía Colombiana ◽

10.15446/agron.colomb.v33n2.50095 ◽

2015 ◽

Vol 33 (2) ◽

pp. 184-193 ◽

Cited By ~ 3

Author(s):

Giovanni Chaves-Bedoya ◽

Luz Yineth Ortiz-Rojas

Keyword(s):

Coat Protein ◽

Genetic Variability ◽

Carica Papaya ◽

Local Level ◽

Bioinformatic Analysis ◽

Ringspot Virus ◽

Limiting Factor ◽

Papaya Ringspot Virus ◽

Phylogenetic Groups ◽

Valle Del Cauca

The Papaya ringspot virus (PRSV), a member of the potyvirus that is transmitted by aphids within the Potyviridae family, is the main limiting factor for papaya (Carica papaya L.) and Cucurbits worldwide and causes losses of up to 100%. In this study, we conducted research on the genetic diversity of PRSV isolates collected from two locations in the department of Norte de Santander, Colombia. The analysis was performed by comparing the nucleotide sequences of the region that encode the coat protein (CP) of nine PRSV isolates from the Villa del Rosario location and 12 isolates from the Campo Hermoso location. The analysis included three sequences of the CP of PRSV isolates reported in the Colombian departments of Arauca and Valle del Cauca. The bioinformatic analysis suggested that the PRSV isolates from the locations in Norte de Santander were different from each other, grouping into different phylogenetic groups. Anexistence of recombination events in the coat protein was observed. This is the first study of PRSV genetic variability that has been conducted at the local level in Colombia.

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Sequences of the coat protein gene from brazilian isolates of Papaya ringspot virus

Fitopatologia Brasileira ◽

10.1590/s0100-41582002000200009 ◽

2002 ◽

Vol 27 (2) ◽

pp. 174-180 ◽

Cited By ~ 7

Author(s):

ROBERTO C. A. LIMA ◽

MANOEL T. SOUZA JR. ◽

GILVAN PIO-RIBEIRO ◽

J. ALBERSIO A. LIMA

Keyword(s):

Coat Protein ◽

Carica Papaya ◽

Protein Gene ◽

Average Degree ◽

Ringspot Virus ◽

Plant Genome ◽

Papaya Ringspot Virus ◽

Transgenic Papaya ◽

Cp Gene ◽

Worldwide Production

Papaya ringspot virus (PRSV) is the causal agent of the main papaya (Carica papaya) disease in the world. Brazil is currently the world's main papaya grower, responsible for about 40% of the worldwide production. Resistance to PRSV on transgenic plants expressing the PRSV coat protein (cp) gene was shown to be dependent on the sequence homology between the cp transgene expressed in the plant genome and the cp gene from the incoming virus, in an isolate-specific fashion. Therefore, knowledge of the degree of homology among the cp genes from distinct PRSV isolates which are present in a given area is important to guide the development of transgenic papaya for the control of PRSV in that area. The objective of the present study was to assess the degree of homology among the PRSV cp genes of several Brazilian isolates of this virus. Papaya and PRSV are present in many different ecosystems within Brazil. Twelve PRSV isolates, collected in eight different states from four different geographic regions, were used in this study. The sequences of the cp gene from these isolates were compared among themselves and to the gene used to generate transgenic papaya for Brazil. An average degree of homology of 97.3% at the nucleotide sequence was found among the Brazilian isolates. When compared to 27 isolates from outside Brazil in a homology tree, the Brazilian isolates were clustered with Australian, Hawaiian, and Central and North American isolates, with an average degree of homology of 90.7% among them.

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High Mutation Frequency and Significant Population Differentiation in Papaya Ringspot Virus-W Isolates

Pathogens ◽

10.3390/pathogens10101278 ◽

2021 ◽

Vol 10 (10) ◽

pp. 1278

Author(s):

Vivek Khanal ◽

Akhtar Ali

Keyword(s):

Geographical Location ◽

Gc Content ◽

Purifying Selection ◽

Ringspot Virus ◽

Papaya Ringspot Virus ◽

Coding Region ◽

Minimal Impact ◽

High Mutation Frequency ◽

Cp Gene ◽

Mutational Hotspots

A total of 101 papaya ringspot virus-W (PRSV-W) isolates were collected from five different cucurbit hosts in six counties of Oklahoma during the 2016–2018 growing seasons. The coat protein (CP) coding region of these isolates was amplified by reverse transcription-polymerase chain reaction, and 370 clones (3–5 clones/isolate) were sequenced. Phylogenetic analysis revealed three phylogroups while host, location, and collection time of isolates had minimal impact on grouping pattern. When CP gene sequences of these isolates were compared with sequences of published PRSV isolates (both P and W strains), they clustered into four phylogroups based on geographical location. Oklahoman PRSV-W isolates formed one of the four distinct major phylogroups. The permutation-based tests, including Ks, Ks *, Z *, Snn, and neutrality tests, indicated significant genetic differentiation and polymorphisms among PRSV-W populations in Oklahoma. The selection analysis confirmed that the CP gene is undergoing purifying selection. The mutation frequencies among all PRSV-W isolates were within the range of 1 × 10−3. The substitution mutations in 370 clones of PRSV-W isolates showed a high proportion of transition mutations, which gave rise to higher GC content. The N-terminal region of the CP gene mostly contained the variable sites with numerous mutational hotspots, while the core region was highly conserved.

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First Report of Papaya ringspot virus–Type W and Zucchini yellow mosaic virus Infecting Trichosanthes cucumerina in Brazil

Plant Disease ◽

10.1094/pdis-94-6-0789b ◽

2010 ◽

Vol 94 (6) ◽

pp. 789-789 ◽

Cited By ~ 4

Author(s):

A. S. Jadão ◽

J. E. Buriola ◽

J. A. M. Rezende

Keyword(s):

Amino Acid ◽

Mosaic Virus ◽

Virus Type ◽

Zucchini Yellow Mosaic Virus ◽

Amino Acid Sequences ◽

Ringspot Virus ◽

Yellow Mosaic Virus ◽

Papaya Ringspot Virus ◽

Mechanical Inoculation ◽

Cp Gene

Trichosanthes cucumerina L., known as snake gourd, is a cucurbitaceous plant that is probably native to and originally domesticated in India. It is cultivated in humid subtropical and tropical countries of Australia, Latin America, and Africa (2). Plants of this species exhibiting symptoms of mosaic and leaf malformation were found during November 2008 near an experimental field of the Departamento de Fitopatologia e Nematologia, Universidade de São Paulo, Piracicaba, State of São Paulo, Brazil. Electron microscopy examination of negatively stained extract of infected tissue showed the presence of filamentous potyvirus-like particles. Sap from these infected plants reacted in plate-trapped antigen (PTA)-ELISA with the antiserum against Papaya ringspot virus–type W (PRSV-W) or Zucchini yellow mosaic virus (ZYMV), but not with the antiserum against Cucumber mosaic virus (CMV) or Zucchini lethal chlorosis virus (ZLCV). PRSV-W and ZYMV were simultaneously transmitted by mechanical inoculation to four plants of Cucurbita pepo cv. Caserta and one plant of T. cucumerina, causing mosaic. In addition, PRSV-W and ZYMV isolates from our virus collection separately infected one plant of T. cucumerina after mechanical inoculation. Infections were confirmed by PTA-ELISA. Total RNA extracted from infected and healthy T. cucumerina was analyzed by reverse transcription (RT)-PCR using a primer pair specific to the coat protein (CP) gene of PRSV-W (4) or ZYMV (3). Fragments of 864 bp and 1,045 bp were amplified with each pair of primers, respectively. Nucleotide sequences directly obtained from purified PCR products were used for further identification of these potyviruses. The nucleotide and deduced amino acid sequences of part of the CP gene (792 nt) of PRSV-W (GenBank Accession No. GU586789) shared 99 and 98% identity, respectively, with that of the Brazilian isolate PRSV-W-C (GenBank Accession No. 4152). The nucleotide and deduced amino acid sequences of the entire CP gene (837 nt) of ZYMV (GenBank Accession No. 6790) shared 91 to 98% and 94 to 100% identity, respectively, with innumerous isolates of ZYMV deposited in the GenBank (e.g., Accession Nos. AB004640, D13914, AB004641, and AJ420019). Natural infection of T. cucumerina by PRSV-W was reported in Nepal (1). To our knowledge, this is the first report of T. cucumerina infected by PRSV-W and ZYMV in Brazil. References: (1) G. Dahal et al. Ann. Appl. Biol. 130:491, 1997. (2) R. W. Robinson and D. S. Decker-Walters. Cucurbits. CAB International, Wallingford, UK. 1997. (3) K. G. Thomson et al. J. Virol. Methods 55:83, 1995. (4) M. G. S. D. Vechia. Fitopatol. Bras. 28:678, 2003.

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Genetic variability and evolutionary dynamics of atypical Papaya ringspot virus infecting Papaya

PLoS ONE ◽

10.1371/journal.pone.0258298 ◽

2021 ◽

Vol 16 (10) ◽

pp. e0258298

Author(s):

Anam Saleem ◽

Zahid Ali ◽

Shyi-Dong Yeh ◽

Wajeeha Saeed ◽

Amna Binat Imdad ◽

...

Keyword(s):

Gene Flow ◽

Genetic Differentiation ◽

Evolutionary Dynamics ◽

Genetic Distances ◽

Full Length ◽

Ringspot Virus ◽

Genomic Sequences ◽

Papaya Ringspot Virus ◽

Cp Gene ◽

Geographical Position

Papaya ringspot virus biotype-P is a detrimental pathogen of economically important papaya and cucurbits worldwide. The mutation prone feature of this virus perhaps accounts for its geographical dissemination. In this study, investigations of the atypical PRSV-P strain was conducted based on phylogenetic, recombination and genetic differentiation analyses considering of it’s likely spread across India and Bangladesh. Full length genomic sequences of 38 PRSV isolates and 35 CP gene sequences were subjected to recombination analysis. A total of 61 recombination events were detected in aligned complete PRSV genome sequences. 3 events were detected in complete genome of PRSV strain PK whereas one was in its CP gene sequence. The PRSV-PK appeared to be recombinant of a major parent from Bangladesh. However, the genetic differentiation based on full length genomic sequences revealed less frequent gene flow between virus PRSV-PK and the population from America, India, Colombia, other Asian Countries and Australia. Whereas, frequent gene flow exists between Pakistan and Bangladesh virus populations. These results provided evidence correlating geographical position and genetic distances. We speculate that the genetic variations and evolutionary dynamics of this virus may challenge the resistance developed in papaya against PRSV and give rise to virus lineage because of its atypical emergence where geographic spread is already occurring.

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Sequence similarity between the viral cp gene and the transgene in transgenic papayas

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2005000500009 ◽

2005 ◽

Vol 40 (5) ◽

pp. 479-486 ◽

Cited By ~ 1

Author(s):

Manoel Teixeira Souza Júnior ◽

Dennis Gonsalves

Keyword(s):

Comparative Analysis ◽

Coat Protein ◽

Transgenic Plants ◽

Sequence Similarity ◽

Ringspot Virus ◽

Papaya Ringspot Virus ◽

High Sequence Similarity ◽

Mechanism Of Resistance ◽

Cp Gene ◽

Do So

The Papaya ringspot virus (PRSV) coat protein transgene present in 'Rainbow' and 'SunUp' papayas disclose high sequence similarity (>89%) to the cp gene from PRSV BR and TH. Despite this, both isolates are able to break down the resistance in 'Rainbow', while only the latter is able to do so in 'SunUp'. The objective of this work was to evaluate the degree of sequence similarity between the cp gene in the challenge isolate and the cp transgene in transgenic papayas resistant to PRSV. The production of a hybrid virus containing the genome backbone of PRSV HA up to the Apa I site in the NIb gene, and downstream from there, the sequence of PRSV TH was undertaken. This hybrid virus, PRSV HA/TH, was obtained and used to challenge 'Rainbow', 'SunUp', and an R2 population derived from line 63-1, all resistant to PRSV HA. PRSV HA/TH broke down the resistance in both papaya varieties and in the 63-1 population, demonstrating that sequence similarity is a major factor in the mechanism of resistance used by transgenic papayas expressing the cp gene. A comparative analysis of the cp gene present in line 55-1 and 63-1-derived transgenic plants and in PRSV HA, BR, and TH was also performed.

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Characterization of a severe isolate of papaya ringspot virus from papaya in western India

Journal of Plant Pathology ◽

10.1007/s42161-019-00340-4 ◽

2019 ◽

Vol 101 (4) ◽

pp. 1203-1209

Author(s):

Asawari Gorane ◽

Raj Verma ◽

Archana Naik ◽

Tukaram Nikam ◽

Avinash Ade ◽

...

Keyword(s):

Ringspot Virus ◽

Western India ◽

Papaya Ringspot Virus ◽

Severe Isolate

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Broad-Spectrum Resistance to Different Geographic Strains of Papaya ringspot virus in Coat Protein Gene Transgenic Papaya

Phytopathology ◽

10.1094/phyto.2003.93.1.112 ◽

2003 ◽

Vol 93 (1) ◽

pp. 112-120 ◽

Cited By ~ 68

Author(s):

Huey-Jiunn Bau ◽

Ying-Huey Cheng ◽

Tsong-Ann Yu ◽

Jiu-Sherng Yang ◽

Shyi-Dong Yeh

Keyword(s):

Coat Protein ◽

Broad Spectrum ◽

Ringspot Virus ◽

Papaya Ringspot Virus ◽

Selected Lines ◽

Cp Gene ◽

Broad Spectrum Resistance ◽

The World ◽

Transgenic Lines ◽

Different Levels

Papaya ringspot virus (PRSV) is a major limiting factor for cultivation of papaya (Carica papaya) in tropical and subtropical areas throughout the world. Although the coat protein (CP) gene of PRSV has been transferred into papaya by particle bombardment and transgenic lines with high resistance to Hawaii strains have been obtained, they are susceptible to PRSV isolates outside of Hawaii. This strain-specific resistance limits the application of the transgenic lines in other areas of the world. In this investigation, the CP gene of a local strain isolated from Taiwan, designated PRSV YK, was transferred into papaya via Agrobacterium-mediated transformation. A total of 45 putative transgenic lines were obtained and the presence of the transgene in papaya was confirmed by polymerase chain reaction amplification. When the plants of transgenic lines were challenged with PRSV YK by mechanical inoculation, they showed different levels of resistance ranging from delay of symptom development to complete immunity. Molecular analysis of nine selected lines that exhibited different levels of resistance revealed that the expression level of the transgene is negatively correlated with the degree of resistance, suggesting that the resistance is manifested by a RNA-mediated mechanism. The segregation analysis showed that the transgene in the immune line 18-0-9 has an inheritance of two dominant loci and the other four highly resistant lines have a single dominant locus. Seven selected lines were tested further for resistance to three PRSV heterologous strains that originated in Hawaii, Thailand, and Mexico. Six of the seven lines showed varying degrees of resistance to the heterologous strains, and one line, 19-0-1, was immune not only to the homologous YK strain but also to the three heterologous strains. Thus, these CP-transgenic papaya lines with broad-spectrum resistance have great potential for use in Taiwan and other geographic areas to control PRSV.

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