1 School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, WA, Australia.
2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia.
Plant Dis. 2019 Apr;103(4):737-747. doi: 10.1094/PDIS-07-18-1136-RE. Epub 2019 Mar 11.
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.
从在巴布亚新几内亚（PNG）东部高地省戈罗卡区的扎格或西部高地省芒特哈根区的巴格生长的表现花叶症状的南瓜（Cucurbita spp.）或黄瓜（Cucumis sativus）植株中分离得到了番木瓜环斑病毒（PRSV）分离物。这些样本被送到澳大利亚的 FTA 卡上，在那里它们进行了高通量测序（HTS）。当通过 HTS 获得的六个新的 PRSV 基因组序列的编码区与来自世界其他地区的 54 个其他完整 PRSV 序列进行比较时，所有六个序列都与澳大利亚的 12 个北部序列一起分组在主要的小类群 B 内的小类群 I，澳大利亚的序列来自三个广泛分散的地点，横跨该大陆的北部。值得注意的是，没有一个 PNG 分离物与来自附近国家东帝汶的小类群 A 基因组序列聚类。澳大利亚和 PNG 序列之间最接近的遗传匹配是核苷酸（nt）序列同一性为 96.9%，而 PNG 和东帝汶分离物之间仅为 83.1%。这些系统发育和 nt 同一性发现表明 PRSV 种群之间存在遗传联系。对 60 个 PRSV 序列进行重组分析发现，在 18 个分离物中有 26 个重组事件的证据，其中只有 4 个在主要的小类群 B 内，而且都不在 PNG 或澳大利亚。在重组基因组中，P1、Cl、NIa-Pro、NIb、6K2 和 5'UTR 区域包含最高数量的重组断点。在去除非重组序列后，丢失了四个小类群（IV、VII、VIII、XV），其中只有一个在小类群 B 内。当从重组体中去除重组衍生序列的基因组区域并在与非重组基因组对齐之前，先前在主要小类群 A 内的七个小类群和主要小类群 B 内的两个小类群，部分或完全合并形成四个合并的小类群。PNG 和澳大利亚北部分离物之间的遗传联系以及两个群体中都没有检测到重组表明，东帝汶的 PRSV 分离物而不是 PNG，可能对澳大利亚北部农业构成生物安全威胁，如果它们比现有的更具毒力。
