The nucleotide sequence of the coat protein gene and 3' untranslated region of papaya ringspot virus type W (Aust)

Genetic Connectivity Between Papaya Ringspot Virus Genomes from Papua New Guinea and Northern Australia, and New Recombination Insights

Isolates of papaya ringspot virus (PRSV) were obtained from plants of pumpkin (Cucurbita spp.) or cucumber (Cucumis sativus) showing mosaic symptoms growing at Zage in Goroka District in the Eastern Highland Province of Papua New Guinea (PNG) or Bagl in the Mount Hagen District, Western Highlands Province. The samples were sent to Australia on FTA cards where they were subjected to High Throughput Sequencing (HTS). When the coding regions of the six new PRSV genomic sequences obtained via HTS were compared with those of 54 other complete PRSV sequences from other parts of the world, all six grouped together with the 12 northern Australian sequences within major phylogroup B minor phylogroup I, the Australian sequences coming from three widely dispersed locations spanning the north of the continent. Notably, none of the PNG isolates grouped with genomic sequences from the nearby country of East Timor in phylogroup A. The closest genetic match between Australian and PNG sequences was a nucleotide (nt) sequence identity of 96.9%, whereas between PNG and East Timorese isolates it was only 83.1%. These phylogenetic and nt identity findings demonstrate genetic connectivity between PRSV populations from PNG and Australia. Recombination analysis of the 60 PRSV sequences available revealed evidence of 26 recombination events within 18 isolates, only four of which were within major phylogroup B and none of which were from PNG or Australia. Within the recombinant genomes, the P1, Cl, NIa-Pro, NIb, 6K2, and 5'UTR regions contained the highest numbers of recombination breakpoints. After removal of nonrecombinant sequences, four minor phylogroups were lost (IV, VII, VIII, XV), only one of which was in phylogroup B. When genome regions from which recombinationally derived tracts of sequence were removed from recombinants prior to alignment with nonrecombinant genomes, seven previous minor phylogroups within major phylogroup A, and two within major phylogroup B, merged either partially or entirely forming four merged minor phylogroups. The genetic connectivity between PNG and northern Australian isolates and absence of detectable recombination within either group suggests that PRSV isolates from East Timor, rather than PNG, might pose a biosecurity threat to northern Australian agriculture should they prove more virulent than those already present.

Papaya ringspot virus Populations From East Timorese and Northern Australian Cucurbit Crops: Biological and Molecular Properties, and Absence of Genetic Connectivity

To examine possible genetic connectivity between crop viruses found in Southeast Asia and Australia, Papaya ringspot virus biotype W (PRSV-W) isolates from cucurbits growing in East Timor and northern Australia were studied. East Timorese samples from cucumber (Cucumis sativus) or pumpkin (Cucurbita moschata and C. maxima) were sent to Australia on FTA cards. These samples and others of pumpkin, rockmelon, honeydew melon (Cucumis melo), or watermelon (Citrullus lanatus) growing in one location each in northwest, north, or northeast Australia were subjected to high throughput sequencing (HTS). When the 17 complete PRSV genomic sequences obtained by HTS were compared with 32 others from GenBank, the five from East Timor were in a different major phylogroup from the 12 Australian sequences. Moreover, the East Timorese and Australian sequences each formed their own minor phylogroups named VI and I, respectively. A Taiwanese sequence was closest to the East Timorese (89.6% nt dentity), and Mexican and Brazilian sequences were the closest to the Australian (92.3% nt identity). When coat protein gene (CP) sequences from the 17 new genomic sequences were compared with 126 others from GenBank, three Australian isolates sequenced more than 20 years ago grouped with the new Australian sequences, while the closest sequence to the East Timorese was from Thailand (93.1% nt identity). Recombination analysis revealed 13 recombination events among the 49 complete genomes. Two isolates from East Timor (TM50, TM32) and eight from GenBank were recombinants, but all 12 Australian isolates were non-recombinants. No evidence of genome connectivity between Australian and Southeast Asian PRSV populations was obtained. The strand-specific RNA library approach used optimized data collection for virus genome assembly. When an Australian PRSV isolate was inoculated to plants of zucchini (Cucurbita pepo), watermelon, rockmelon, and honeydew melon, they all developed systemic foliage symptoms characteristic of PRSV-W, but symptom severity varied among melon cultivars.

Control of papaya ringspot virus in papaya: a case study

The papaya crop is severely affected by papaya ringspot virus (PSRV) worldwide. This review focuses on efforts to control the destructiveness of the disease caused by PSRV in Hawaii, starting from the use of cross protection to parasite-derived resistance with transgenic papaya expressing the PSRV coat protein gene. A chronology of the research effort is given and related to the development of technologies and the pressing need to control PSRV in Hawaii. The development of commercial virus-resistant transgenic papaya provides a tangible approach to control PSRV in Hawaii. Moreover, the development of transgenic papaya by other laboratories and employment of a mechanism of effective technology transfer to different countries hold promise for control of PSRV worldwide.

Nucleotide sequence of the capsid protein gene of papaya leaf-distortion mosaic potyvirus

The DNA complementary to the 3'-terminal 1 404 nucleotides [excluding the poly(A) tail] of papaya leaf-distortion mosaic potyvirus (PLDMV) RNA was cloned and sequenced. The sequence starts within a long open reading frame (ORF) of 1 195 nucleotides and is followed by a 3' non-coding region of 209 nucleotides. Capsid protein (CP) is encoded at the 3' terminus of the ORF. The CP contains 293 residues and has a Mr of 33 277. The CP of PLDMV exhibits 49 to 59% sequence similarity at the amino acid level to the CPs of papaya ringspot potyvirus (PRSV) and other potyviruses. This result is consistent with the absence of a serological relationship between PLDMV and PRSV or other potyviruses. The results support the assignment of PLDMV as a distinct member of the genus Potyvirus.