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

Pathogens ◽  
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.

scholarly journals Comparative reactions of recombinant papaya ringspot viruses with chimeric coat protein (CP) genes and wild-type viruses on CP-transgenic papaya

2001 ◽  
Vol 82 (11) ◽  
pp. 2827-2836 ◽  
Author(s):  
Chu-Hui Chiang ◽  
Ju-Jung Wang ◽  
Fuh-Jyh Jan ◽  
Shyi-Dong Yeh ◽  
Dennis Gonsalves
Keyword(s):  
Coat Protein ◽  
Sequence Similarity ◽  
Transcriptional Gene Silencing ◽  
Papaya Ringspot Virus ◽  
Wild Type ◽  
Coding Region ◽  
Transgenic Papaya ◽  
Cp Gene ◽  
Post Transcriptional Gene Silencing

Transgenic papaya cultivars SunUp and Rainbow express the coat protein (CP) gene of the mild mutant of papaya ringspot virus (PRSV) HA. Both cultivars are resistant to PRSV HA and other Hawaii isolates through homology-dependent resistance via post-transcriptional gene silencing. However, Rainbow, which is hemizygous for the CP gene, is susceptible to PRSV isolates from outside Hawaii, while the CP-homozygous SunUp is resistant to most isolates but susceptible to the YK isolate from Taiwan. To investigate the role of CP sequence similarity in overcoming the resistance of Rainbow, PRSV HA recombinants with various CP segments of the YK isolate were constructed and evaluated on Rainbow, SunUp and non-transgenic papaya. Non-transgenic papaya were severely infected by all recombinants, but Rainbow plants developed a variety of symptoms. On Rainbow, a recombinant with the entire CP gene of YK caused severe symptoms, while recombinants with only partial YK CP sequences produced a range of milder symptoms. Interestingly, a recombinant with a YK segment from the 5′ region of the CP gene caused very mild, transient symptoms, whereas recombinants with YK segments from the middle and 3′ parts of the CP gene caused prominent and lasting symptoms. SunUp was resistant to all but two recombinants, which contained the entire CP gene or the central and 3′-end regions of the CP gene and the 3′ non-coding region of YK, and the resulting symptoms were mild. It is concluded that the position of the heterologous sequences in the recombinants influences their pathogenicity on Rainbow.

scholarly journals Engineered Resistance Against Papaya ringspot virus in Venezuelan Transgenic Papayas

Plant Disease ◽  
2004 ◽  
Vol 88 (5) ◽  
pp. 516-522 ◽  
Author(s):  
Gustavo Fermin ◽  
Valentina Inglessis ◽  
Cesar Garboza ◽  
Sairo Rangel ◽  
Manuel Dagert ◽  
...  
Keyword(s):  
Amino Acid ◽  
Agrobacterium Tumefaciens ◽  
Coat Protein ◽  
Amino Acid Sequence ◽  
Sequence Similarity ◽  
Ringspot Virus ◽  
Amino Acid Sequence Similarity ◽  
Papaya Ringspot Virus ◽  
Local Varieties ◽  
Cp Gene

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.

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

2003 ◽  
Vol 28 (6) ◽  
pp. 678-681 ◽  
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.

scholarly journals Mutation bias shapes gene evolution in Arabidopsis thaliana

2020 ◽  
Author(s):  
J. Grey Monroe ◽  
Thanvi Srikant ◽  
Pablo Carbonell-Bejerano ◽  
Moises Exposito-Alonso ◽  
Mao-Lun Weng ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
De Novo ◽  
Gene Evolution ◽  
Gc Content ◽  
Mutation Rates ◽  
Rate Variation ◽  
Recent Theory ◽  
De Novo Mutations ◽  
Coding Region ◽  
Mutational Hotspots

Classical evolutionary theory maintains that mutation rate variation between genes should be random with respect to fitness 1–4 and evolutionary optimization of genic mutation rates remains controversial 3,5. However, it has now become known that cytogenetic (DNA sequence + epigenomic) features influence local mutation probabilities 6, which is predicted by more recent theory to be a prerequisite for beneficial mutation rates between different classes of genes to readily evolve 7. To test this possibility, we used de novo mutations in Arabidopsis thaliana to create a high resolution predictive model of mutation rates as a function of cytogenetic features across the genome. As expected, mutation rates are significantly predicted by features such as GC content, histone modifications, and chromatin accessibility. Deeper analyses of predicted mutation rates reveal effects of introns and untranslated exon regions in distancing coding sequences from mutational hotspots at the start and end of transcribed regions in A. thaliana. Finally, predicted coding region mutation rates are significantly lower in genes where mutations are more likely to be deleterious, supported by numerous estimates of evolutionary and functional constraint. These findings contradict neutral expectations that mutation probabilities are independent of fitness consequences. Instead they are consistent with the evolution of lower mutation rates in functionally constrained loci due to cytogenetic features, with important implications for evolutionary biology8.

scholarly journals Generation of Transgenic Papaya with Double Resistance to Papaya ringspot virus and Papaya leaf-distortion mosaic virus

2009 ◽  
Vol 99 (11) ◽  
pp. 1312-1320 ◽  
Author(s):  
Yi-Jung Kung ◽  
Huey-Jiunn Bau ◽  
Yi-Ling Wu ◽  
Chiung-Huei Huang ◽  
Tsui-Miao Chen ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Field Tests ◽  
Ringspot Virus ◽  
Papaya Ringspot Virus ◽  
Coding Region ◽  
Transgenic Papaya ◽  
Resistant Lines ◽  
Transgenic Lines ◽  
Chimeric Construct ◽  
Leaf Distortion

During the field tests of coat protein (CP)-transgenic papaya lines resistant to Papaya ringspot virus (PRSV), another Potyvirus sp., Papaya leaf-distortion mosaic virus (PLDMV), appeared as an emerging threat to the transgenic papaya. In this investigation, an untranslatable chimeric construct containing the truncated CP coding region of the PLDMV P-TW-WF isolate and the truncated CP coding region with the complete 3′ untranslated region of PRSV YK isolate was transferred into papaya (Carica papaya cv. Thailand) via Agrobacterium-mediated transformation to generate transgenic plants with resistance to PLDMV and PRSV. Seventy-five transgenic lines were obtained and challenged with PRSV YK or PLDMV P-TW-WF by mechanical inoculation under greenhouse conditions. Thirty-eight transgenic lines showing no symptoms 1 month after inoculation were regarded as highly resistant lines. Southern and Northern analyses revealed that four weakly resistant lines have one or two inserts of the construct and accumulate detectable amounts of transgene transcript, whereas nine resistant lines contain two or three inserts without significant accumulation of transgene transcript. The results indicated that double virus resistance in transgenic lines resulted from double or more copies of the insert through the mechanism of RNA-mediated posttranscriptional gene silencing. Furthermore, three of nine resistant lines showed high levels of resistance to heterologous PRSV strains originating from Hawaii, Thailand, and Mexico. Our transgenic lines have great potential for controlling a number of PRSV strains and PLDMV in Taiwan and elsewhere.

scholarly journals Genetic variability and evolutionary dynamics of atypical Papaya ringspot virus infecting Papaya.

2020 ◽  
Author(s):  
Anam Saleem ◽  
Zahid Ali ◽  
Shyi-Dong Yeh ◽  
Wajeeha Saeed ◽  
Amna Imdad ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Ringspot Virus ◽  
Papaya Ringspot Virus ◽  
Coding Region ◽  
Amino Terminal ◽  
North East ◽  
East Region ◽  
Geographic Spread ◽  
Amino Acid Levels ◽  
Helper Component Proteinase

Abstract The mutation prone RNA genome of Papaya ringspot virus could be a driving force behind its geographical spread and dissemination. Here we present the molecular investigations on atypical PRSV–P strain identified from Pakistan with genome sequence phylogenetic and recombination analysis. The PRSV-P, Pakistan outbreak strain showing a geographic spread across India and Bangladesh in phylogenetic lineage. In major recombination events, it has acquired genome variation in amino terminal of PRSV coat protein gene, whereas the gene for helper component-proteinase (HC–Pro), a nonstructural coding region of multi-domain provenance, also evolves at nucleotide and amino acid levels. The phylogenetic analysis of another highly variable P1 region showed evolutionary dynamics with respect to other geographical strains, particularly the Indian isolate from North East region (Meghalaya). PRSV–PK holds high levels of genetic divergence in comparison to American, Australian and Asian isolates. The genetic and phylogeographic analyses indicate that a spatial recombination has occurred from first PRSV, however temporal evolution is within the region of occurrence. 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.

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

2002 ◽  
Vol 27 (2) ◽  
pp. 174-180 ◽  
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.

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

Plant Disease ◽  
2010 ◽  
Vol 94 (6) ◽  
pp. 789-789 ◽  
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.

scholarly journals Comparative analyses of 32 complete plastomes of Tef (Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9314
Author(s):  
Girma Eshetu Teshome ◽  
Yeshitila Mekbib ◽  
Guangwan Hu ◽  
Zhi-Zhong Li ◽  
Jinming Chen
Keyword(s):  
Phylogenetic Analyses ◽  
Gc Content ◽  
Purifying Selection ◽  
Breeding Population ◽  
Rrna Genes ◽  
Eragrostis Tef ◽  
Protein Coding ◽  
Mutational Hotspots ◽  
Genomic Resource ◽  
Genomic Regions

Eragrostis tef is an important cereal crop in Ethiopia with excellent storage properties, high–quality food, and the unique ability to thrive in extreme environmental conditions. However, the application of advanced molecular tools for breeding and conservation of these species is extremely limited. Therefore, developing chloroplast genome resources and high-resolution molecular markers are valuable to E. tef population and biogeographic studies. In the current study, we assembled and compared the complete plastomes of 32 E. tef accessions. The size of the plastomes ranged from 134,349 to 134,437 bp with similar GC content (∼38.3%). Genomes annotations revealed 112 individual genes, including 77 protein-coding, 31 tRNA, and 4 rRNA genes. Comparison of E. tef plastomes revealed a low degree of intraspecific sequence variations and no structural differentiations. Furthermore, we found 34 polymorphic sites (13 cpSSRs, 12 InDels, and 9 SNPs) that can be used as valuable DNA barcodes. Among them, the majority (88%) of the polymorphic sites were identified in the noncoding genomic regions. Nonsynonymous (ka) and synonymous (ks) substitution analysis showed that all PCGs were under purifying selection (ka/ks <1). The phylogenetic analyses of the whole plastomes and polymorphic region sequences were able to distinguish the accession from the southern population, indicating its potential to be used as a super-barcode. In conclusion, the newly generated plastomes and polymorphic markers developed here could be a useful genomic resource in molecular breeding, population genetics and the biogeographical study of E. tef.

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