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Zucchini yellow mosaic virus (ZYMV) isolates were obtained in Papua New Guinea (PNG) from cucumber (Cucumis sativus) or pumpkin (Cucurbita spp.) plants showing mosaic symptoms growing at Kongop in the Mount Hagen District, Western Highlands Province, or Zage in the Goroka District, Eastern Highlands Province. The samples were blotted onto FTA cards, which were sent to Australia, where they were subjected to high-throughput sequencing. When the coding regions of the nine new ZYMV genomic sequences found were compared with those of 64 other ZYMV sequences from elsewhere, they grouped together, forming new minor phylogroup VII within ZYMV’s major phylogroup A. Genetic connectivity was lacking between ZYMV genomic sequences from PNG and its neighboring countries, Australia and East Timor; the closest match between a PNG and any other genomic sequence was a 92.8% nucleotide identity with a sequence in major phylogroup A’s minor phylogroup VI from Japan. When the RDP5.2 recombination analysis program was used to compare 66 ZYMV sequences, evidence was obtained of 30 firm recombination events involving 41 sequences, and all isolates from PNG were recombinants. There were 21 sequences without recombination events in major phylogroup A, whereas there were only 4 such sequences within major phylogroup B. ZYMV’s P1, Cl, N1a-Pro, P3, CP, and NIb regions contained the highest evidence of recombination breakpoints. Following removal of recombinant sequences, seven minor phylogroups were absent (I, III, IV, V, VI, VII, and VIII), leaving only minor phylogroups II and IX. By contrast, when a phylogenetic tree was constructed using recombinant sequences with their recombinationally derived tracts removed before analysis, five previous minor phylogroups remained unchanged within major phylogroup A (II, III, IV, V, and VII) while four formed two new merged phylogroups (I/VI and VIII/IX). Absence of genetic connectivity between PNG, Australian, and East Timorese ZYMV sequences, and the 92.8% nucleotide identity between a PNG sequence and the closest sequence from elsewhere, suggest that a single introduction may have occurred followed by subsequent evolution to adapt to the PNG environment. The need for enhanced biosecurity measures to protect against potentially damaging virus movements crossing the seas separating neighboring countries in this region of the world is discussed.

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.

Hyaloperonospora brassicae causes downy mildew, a major disease of Brassicaceae species. We sequenced the genomes of two H. brassicae isolates of high (Sample B) and low (Sample C) virulence. Sequencing reads were first assembled de novo with software's SOAPdenovo2, ABySS V2.1 and Velvet V1.1 and later combined to create meta-assemblies with genome sizes of 72.762 and 76.950Mb and predicted gene densities of 1628 and 1644 /Mb, respectively. We could annotate 12.255 and 13,030 genes with high proportions (91-92%) of complete BUSCOs for Sample B and C, respectively. Comparative analysis revealed conserved and varied molecular machinery underlying the physiological specialisation and infection capabilities. BLAST analysis against PHI gene database suggested a relatively higher loss of genes for virulence and pathogenicity in Sample C compared to Sample B, reflecting pathogen evolution through differential rates of mutation and selection. These studies will enable identification and monitoring of H. brassicae virulence factors prevailing in-field.

Globally, high-throughput sequencing (HTS) has been used for virus detection in germplasm certification programs. However, sequencing costs have impeded its implementation as a routine diagnostic certification tool. In this study, the targeted genome sequencing (TG-Seq) approach was developed to simultaneously detect multiple (four) viral species of, Pea early browning virus (PEBV), Cucumber mosaic virus (CMV), Bean yellow mosaic virus (BYMV) and Pea seedborne mosaic virus (PSbMV). TG-Seq detected all the expected viral amplicons within multiplex PCR (mPCR) reactions. In contrast, the expected PCR amplicons were not detected by gel electrophoresis (GE). For example, for CMV, GE only detected RNA1 and RNA2 while TG-Seq detected all the three RNA components of CMV. In an mPCR to amplify all four viruses, TG-Seq readily detected each virus with more than 732,277 sequence reads mapping to each amplicon. In addition, TG-Seq also detected all four amplicons within a 10−8 serial dilution that were not detectable by GE. Our current findings reveal that the TG-Seq approach offers significant potential and is a highly sensitive targeted approach for detecting multiple plant viruses within a given biological sample. This is the first study describing direct HTS of plant virus mPCR products. These findings have major implications for grain germplasm healthy certification programs and biosecurity management in relation to pathogen entry into Australia and elsewhere.

Garlic is one of the most crucial Allium vegetables used as seasoning of foods. It has a lot of benefits from the medicinal and nutritional point of view; however, its production is highly constrained by both biotic and abiotic challenges. Among these, viral infections are the most prevalent factors affecting crop productivity around the globe. This experiment was conducted on eleven selected garlic accessions and three improved varieties collected from different garlic growing agro-climatic regions of Ethiopia. This study aimed to identify and characterize the isolated garlic virus using the coat protein (CP) gene and further determine their phylogenetic relatedness. RNA was extracted from fresh young leaves, thirteen days old seedlings, which showed yellowing, mosaic, and stunting symptoms. Pairwise molecular diversity for CP nucleotide and amino acid sequences were calculated using MEGA5. Maximum Likelihood tree of CP nucleotide sequence data of Allexivirus and Potyvirus were conducted using PhyML, while a neighbor-joining tree was constructed for the amino acid sequence data using MEGA5. From the result, five garlic viruses were identified viz. Garlic virus C (78.6 %), Garlic virus D (64.3 %), Garlic virus X (78.6 %), Onion yellow dwarf virus (OYDV) (100%), and Leek yellow stripe virus (LYSV) (78.6 %). The study revealed the presence of complex mixtures of viruses with 42.9 % of the samples had co-infected with a species complex of Garlic virus C, Garlic virus D, Garlic virus X, OYDV, and LYSV. Pairwise comparisons of the isolated Potyviruses and Allexiviruses species revealed high identity with that of the known members of their respected species. As an exception, less within species identity was observed among Garlic virus C isolates as compared with that of the known members of the species. Finally, our results highlighted the need for stepping up a working framework to establish virus-free garlic planting material exchange in the country which could result in the reduction of viral gene flow across the country.Author SummaryGarlic viruses are the most devastating disease since garlic is the most vulnerable crop due to their vegetative nature of propagation. Currently, the garlic viruses are the aforementioned production constraint in Ethiopia. However, so far very little is known on the identification, diversity, and dissemination of garlic infecting viruses in the country. Here we explore the prevalence, genetic diversity, and the presence of mixed infection of garlic viruses in Ethiopia using next generation sequencing platform. Analysis of nucleotide and amino acid sequences of coat protein genes from infected samples revealed the association of three species from Allexivirus and two species from Potyvirus in a complex mixture. Ultimately the article concludes there is high time to set up a working framework to establish garlic free planting material exchange platform which could result in a reduction of viral gene flow across the country.

Busseola fusca (Fuller) (Lepidoptera: Noctuidae), the maize stalk borer, is a widespread crop pest in sub-Saharan Africa that has been the focus of biological research and intensive management strategies. Here, we present a comprehensive annotated transcriptome of B. fusca (originally collected in the Western Province of Kenya) based on ten pooled libraries including a wide array of developmental stages, tissue types, and exposures to parasitoid wasps. Parasitoid wasps have been used as a form of biocontrol to try and reduce crop losses with variable success, in part due to differential infectivities and immune responses among wasps and hosts. We identified a number of loci of interest for pest management, including genes potentially involved in chemoreception, immunity, and response to insecticides. The comprehensive sampling design used expands our current understanding of the transcriptome of this species and deepens the list of potential target genes for future crop loss mitigation, in addition to highlighting candidate loci for differential expression and functional genetic analyses in this important pest species.

Pea early browning virus (PEBV) is transmitted by soil-inhabiting trichodorid nematodes and via seeds. The transcriptome sequencing method, followed by de novo assembly, revealed the PEBV Libyan isolate LyV66-91 genome. Its RNA1 resembled that of UK isolate SP5 with 93.91% nucleotide identity, and its RNA2 had 63.32% nucleotide identity to that of Dutch isolate E116.

Sweet potato feathery mottle virus (SPFMV) and Sweet potato virus C (SPVC) isolates were obtained from sweetpotato shoot or tuberous root samples from three widely separated locations in Australia’s tropical north (Cairns, Darwin, and Kununurra). The samples were planted in the glasshouse and scions obtained from the plants were graft inoculated to Ipomoea setosa plants. Virus symptoms were recorded in the field in Kununurra and in glasshouse-grown sweetpotato and I. setosa plants. RNA extracts from I. setosa leaf samples were subjected to high-throughput sequencing. New complete SPFMV (n = 17) and SPVC (n = 6) genomic sequences were obtained and compared with 47 sequences from GenBank. Phylogenetic analysis revealed that the 17 new SPFMV genomes all fitted within either major phylogroup A, minor phylogroup II, formerly O; or major phylogroup B, formerly RC. Major phylogroup A’s minor phylogroup I, formerly EA, only appeared when recombinants were included. Numbers of SPVC genomes were insufficient to subdivide it into phylogroups. Within phylogroup A’s minor phylogroup II, the closest genetic match between an Australian and a Southeast Asian SPFMV sequence was the 97.4% nucleotide identity with an East Timorese sequence. Recombination analysis of the 43 SPFMV and 27 SPVC sequences revealed evidence of 44 recombination events, 16 of which involved interspecies sequence transfers between SPFMV and SPVC and 28 intraspecies transfers, 17 in SPFMV and 11 in SPVC. Within SPFMV, 11 intraspecies recombination events were between different major phylogroups and 6 were between members of the same major phylogroup. Phylogenetic analysis accounting for the detected recombination events within SPFMV sequences yielded evidence of minor phylogroup II and phylogroup B but the five sequences from minor phylogroup I were distributed in two separate groups among the sequences of minor phylogroup II. For the SPVC sequences, phylogenetic analysis accounting for the detected recombination events revealed three major phylogroups (A, B, and C), with major phylogroup A being further subdivided into two minor phylogroups. Within the recombinant genomes of both viruses, their PI, NIa-Pro, NIb, and CP genes contained the highest numbers of recombination breakpoints. The high frequency of interspecies and interphylogroup recombination events reflects the widespread occurrence of mixed SPVC and SPFMV infections within sweetpotato plants. The prevalence of infection in northern Australian sweetpotato samples reinforces the need for improved virus testing in healthy sweetpotato stock programs. Furthermore, evidence of genetic connectivity between Australian and East Timorese SPFMV genomes emphasizes the need for improved biosecurity measures to protect against potentially damaging international virus movements.

Biological characteristics of 11 Potato virus S (PVS) isolates from three cultivated potato species (Solanum spp.) growing in five Andean countries and 1 from Scotland differed in virulence depending on isolate and host species. Nine isolates infected Chenopodium quinoa systemically but two others and the Scottish isolate remained restricted to inoculated leaves; therefore, they belonged to biologically defined strains PVSA and PVSO, respectively. When nine wild potato species were inoculated, most developed symptomless systemic infection but Solanum megistacrolobum developed systemic hypersensitive resistance (SHR) with one PVSO and two PVSA isolates. Andean potato cultivars developed mostly asymptomatic primary infection but predominantly symptomatic secondary infection. In both wild and cultivated potato plants, PVSA and PVSO elicited similar foliage symptoms. Following graft inoculation, all except two PVSO isolates were detected in partially PVS-resistant cultivar Saco, while clone Snec 66/139-19 developed SHR with two isolates each of PVSA and PVSO. Myzus persicae transmitted all nine PVSA isolates but none of the three PVSO isolates. All 12 isolates were transmitted by plant-to-plant contact. In infective sap, all isolates had thermal inactivation points of 55 to 60°C. Longevities in vitro were 25 to 40 days with six PVSA isolates but less than 21 days for the three PVSO isolates. Dilution end points were 10−3 for two PVSO isolates but 10−4 to 10−6 with the other isolates. Complete new genome sequences were obtained from seven Andean PVS isolates; seven isolates from Africa, Australia, or Europe; and single isolates from S. muricatum and Arracacia xanthorhiza. These 17 new genomes and 23 from GenBank provided 40 unique sequences; however, 5 from Eurasia were recombinants. Phylogenetic analysis of the 35 nonrecombinants revealed three major lineages, two predominantly South American (SA) and evenly branched and one non-SA with a single long basal branch and many distal subdivisions. Using least squares dating and nucleotide sequences, the two nodes of the basal PVS trifurcation were dated at 1079 and 1055 Common Era (CE), the three midphylogeny nodes of the SA lineages at 1352, 1487, and 1537 CE, and the basal node to the non-SA lineage at 1837 CE. The Potato rough dwarf virus/Potato virus P (PVS/PRDV/PVP) cluster was sister to PVS and diverged 5,000 to 7,000 years ago. The non-SA PVS lineage contained 18 of 19 isolates from S. tuberosum subsp. tuberosum but the two SA lineages contained 6 from S. tuberosum subsp. andigena, 4 from S. phureja, 3 from S. tuberosum subsp. tuberosum, and 1 each from S. muricatum, S. curtilobum, and A. xanthorrhiza. This suggests that a potato-infecting proto-PVS/PRDV/PVP emerged in South America at least 5,000 years ago, became endemic, and diverged into a range of local Solanum spp. and other species, and one early lineage spread worldwide in potato. Preventing establishment of the SA lineages is advised for all countries still without them.

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.

Using RNA strand-specific sequencing followed by de novo assembly, a Bean yellow mosaic virus (BYMV) genome was obtained from a lentil sample (Aus14BY) collected in Victoria, Australia, in 2005. When compared with 51 BYMV genomes, it closely resembled the Western Australian isolate PN83A (Lupinus angustifolius), with 98.4% nucleotide identity.

Coding-complete sequences of two barley virus G isolates from Australia were obtained from a 34-year-old oat sample (isolate Aus8) and a 1-year-old barley sample (isolate Aus17N). The Aus8 and Aus17N isolates share 96.3% nucleotide identity with each other and 95.7 to 95.8% nucleotide identity with the South Korean isolate Uiseong.

BackgroundThe African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops.ResultsWe assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome.ConclusionsThe genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family.

Here, we report the first nearly complete genome sequence of Alfalfa mosaic virus (AMV) obtained from a symptomatic field pea sample (Aus295) in Australia. Its genome RNA1 and RNA2 segments resembled those of the Argentinian isolate Manfredi, with 99.4% and 96.7% nucleotide (nt) identity, respectively; its RNA3 segment resembled that of Chinese isolate AMV-Gyn, with 99.6% nt identity.

The maize stalk borer, Busseola fusca, is an important Lepidopteran pest of cereal crops in Central, East, and Southern Africa. Crop losses due to B. fusca feeding activity vary by region, but can result in total crop loss in areas with high levels of infestation. Genomic resources provide critical insight into the biology of pest species and can allow for the development of effective management tools and strategies to mitigate their impact on agriculture. To this end, we sequenced, assembled, and annotated the genome of B. fusca. The total assembled genome size was 492.9 Mb with 19,417 annotated protein-coding genes. Using a comparative approach, we identified a putative expansion in the Chorion gene family, which is involved in the formation of the egg shell structure. Our analysis revealed high repeat content within the B. fusca genome, with LTR sequences comprising the majority of the repetitive sequence. We hope genomic resources will provide a foundation for future work aimed at developing an integrated pest management strategy to reduce B. fusca’s impact on food security.

Zucchini yellow mosaic virus (ZYMV) isolates from cucurbit crops growing in northern Australia and East Timor were investigated to establish possible genetic connectivity between crop viruses in Australia and Southeast Asia. Leaves from symptomatic plants of pumpkin (Cucurbita moschata and C. maxima), melon (Cucumis melo), and zucchini (C. pepo) were sampled near Broome, Darwin, and Kununurra in northern Australia. Leaves from symptomatic plants of cucumber (C. sativus) and pumpkin sampled in East Timor were sent to Australia on FTA cards. These samples were subjected to high-throughput sequencing and 15 complete new ZYMV genomic sequences obtained. When their nucleotide sequences were compared with those of 48 others from GenBank, the East Timorese and Kununurra sequences (three per location) and single earlier sequences from Singapore and Reunion Island were all in major phylogroup B. The seven Broome and two Darwin sequences were in minor phylogroups I and II, respectively, within larger major phylogroup A. When coat protein (CP) nucleotide sequences from the 15 new genomes and 47 Australian isolates sequenced previously were compared with 331 other CP sequences, the closest genetic match for a sequence from Kununurra was with an East Timorese sequence (95.5% nucleotide identity). Analysis of the 63 complete genomes found firm recombination events in 12 (75%) and 2 (4%) sequences from northern Australia or Southeast Asia versus the rest of the world, respectively; therefore, the formers’ high recombination frequency might reflect adaptation to tropical conditions. Both parents of the recombinant Kununurra sequence were East Timorese. Phylogenetic analysis, nucleotide sequence identities, and recombination analysis provided clear evidence of genetic connectivity between sequences from Kununurra and East Timor. Inoculation of a Broome isolate to zucchini and watermelon plants reproduced field symptoms observed in northern Australia. This research has important biosecurity implications over entry of damaging viral crop pathogens not only into northern Australia but also moving between Australia’s different agricultural regions.

A new resistance-breaking strain of Turnip mosaic virus (TuMV) overcomes TuMV resistance genes that currently suppress spread of this virus in Brassica napus crops in the Liverpool Plains region of eastern Australia. Isolates 12.1 and 12.5 of this strain and three other isolates in TuMV pathotypes 1 (NSW-2), 7 (NSW-1), and 8 (WA-Ap1) were inoculated to plants of 19 B. napus cultivars and one breeding line. All plants of these cultivars and the breeding line proved susceptible to 12.1 and 12.5 but developed only resistance phenotypes with WA-Ap1 or mostly resistance phenotypes with NSW-1 and NSW-2. Five different TuMV resistance phenotypes occurred either alone or segregating in different combinations. When these five isolates were inoculated to plants of nine other crop or wild Brassicaceae spp. and four indicator hosts in other families, 12.1 and 12.5 resembled the other three in inducing TuMV resistance phenotypes in some Brassicaceae spp. but not others, and by inducing extreme resistance phenotypes in all inoculated plants of B. oleracea var. botrytis and Raphanus sativus. Therefore, the overall resistance-breaking properties of 12.1 and 12.5 were restricted to B. napus. When isolates 12.1, 12.5, and WA-Ap1 and additional Australian isolate WA-EP1 were sequenced and complete genomes of each compared, 12.1 and 12.5 grouped separately from the other 2 and from all 23 Australian isolates with complete genomes sequenced previously. In addition, there was evidence for at least six separate TuMV introductions to Australia. Spread of this B. napus resistance-breaking strain poses a significant threat to the B. napus oilseed industry. Breeding B. napus cultivars with resistance to this strain constitutes a critical priority for B. napus breeding programs in Australia and elsewhere.

Sweet potato feathery mottle virus (SPFMV) and Sweet potato virus C (SPVC) isolates from sweetpotato were studied to examine genetic connectivity between viruses from Australia and Southeast Asia. East Timorese samples from sweetpotato were sent to Australia on FTA cards. Shoot and tuberous root samples were collected in Australia and planted in the glasshouse, and scions were graft inoculated to Ipomoea setosa plants. Symptoms in infected sweetpotato and I. setosa plants were recorded. RNA extracts from FTA cards and I. setosa leaf samples were subjected to high-throughput sequencing (HTS). Complete genomic sequences (CS) of SPFMV and SPVC (11 each) were obtained by HTS, and coat protein (CP) genes from them were compared with others from GenBank. SPFMV sequences clustered into two major phylogroups (A and B = RC) and two minor phylogroups (EA[I] and O[II]) within A; East Timorese sequences were in EA(I) and O(II), whereas Australian sequences were in O(II) and B(RC). With SPVC, CP trees provided sufficient diversity to distinguish major phylogroups A and B and six minor phylogroups within A (I to VI); East Timorese sequences were in minor phylogroup I, whereas Australian sequences were in minor phylogroups II and VI and in major phylogroup B. With SPFMV, Aus13B grouped with East Timorese sequence TM64B within minor phylogroup O, giving nucleotide sequence identities of 97.4% (CS) and 98.3% (CP). However, the closest match with an Australian sequence was the 97.6% (CS) and 98.7% (CP) nucleotide identity between Aus13B and an Argentinian sequence. With SPVC, closest nucleotide identity matches between Australian and East Timorese sequences were 94.1% with Aus6a and TM68A (CS) and 96.3% with Aus55-4C and TM64A (CP); however neither pair member belonged to the same minor phylogroup. Also, the closest Australian match was 99.1% (CP) nucleotide identity between Aus4C and New Zealand isolate NZ4-4. These first complete genome sequences of SPFMV and SPVC from sweetpotato plantings in the Australian continent and neighboring Southeast Asia suggest at least two (SPFMV) and three (SPVC) separate introductions to Australia since agriculture commenced more than two centuries ago. These findings have major implications for both healthy stock programs and biosecurity management in relation to pathogen entry into Australia and elsewhere.

Unfortunately, the original article was online published with error in the results section. The error is correction by this erratum.

This project sought to investigate the domestic caprid rumen virome by developing a robust viral DNA isolation and enrichment protocol (utilizing membrane filtration, ultra-centrifugation, overnight PEG treatment and nuclease treatment) and using RSD-PCR and high throughput sequencing (HTS) techniques. 3.53% of the reads obtained were analogous to those of viruses denoting Siphoviridae, Myoviridae, Podoviridae, Mimiviridae, Microviridae, Poxviridae, Tectiviridae and Marseillevirus. Most of the sequenced reads from the rumen were similar to those of phages, which are critical in maintaining the rumen microbial populations under its carrying capacity. Though identified in the rumen, most of these viruses have been reported in other environments as well. Improvements in the viral DNA enrichment and isolation protocol are required to obtain data that are more representative of the rumen virome. The 102,130 unknown reads (92.31%) for the goat and 36,241 unknown reads (93.86%) for the sheep obtained may represent novel genomes that need further study.

Gbodo is a traditional Nigerian fermented dried yam food using tubers or slices. Identification of microbes using conventional methods reveals only a fraction of the true microbial community. Forty-five fungal isolates associated with gbodo at 0, 6, 12, 18, and 24 h of steeping/fermentation were identified using molecular techniques. Ribosomal RNA-ITS fragments of genomic DNA were amplified using ITS1 and ITS4 primers and subjected to nuclecotide sequence determination. Meyerozyma gulliermondii represented 56–78% of isolates during 24 h of yam steeping. Sixty-seven percent of all identified isolates were members of the genera Meyerozyma and Pichia. The biodiversity index of fungal isolates increased from 0.33 at 0 h to 0.56 at 12 h. M. guilliermondii exhibited a resilient presence in isolates.

Analysis of an RNA-Seq library from cucumber leaf RNA revealed the first complete genome sequence of Cucurbit aphid-borne yellows virus (CABYV) from Papua New Guinea. We compared it with 36 complete CABYV genomes from other world regions. It most resembled the genome of South Korean isolate GS6.

Thrips have been recognized as primary vectors of tomato spotted wilt virus (TSWV) with Frankliniella occidentalis (Pergande) reported as the most important and efficient vector, while other species such as Thrips tabaci Lindeman also include populations that can vector the virus. A study was undertaken to establish the diversity of thrips and presence of vectors for TSWV in four major tomato production areas in Kenya. The cytochrome oxidase 1 (CO1) gene was used to generate sequences from thrips samples collected from tomatoes and weeds, and phylogenetic analysis done to establish the variation within potential vector populations. Ceratothripoides brunneus Bagnall was the predominant species of thrips in all areas. F. occidentalis and T. tabaci were abundant in Nakuru, Kirinyaga, and Loitokitok but not detected at Bungoma. Other vectors of tospoviruses identified in low numbers were Frankliniella schultzei (Trybom) and Scirtothrips dorsalis Hood. Variation was observed in T. tabaci, F. occidentalis, and F. schultzei. Kenyan specimens of T. tabaci from tomato belonged to the arrhenotokous group, while those of F. occidentalis clustered with the Western flower thrips G group. The detection of RNA of TSWV in both of these species of thrips supported the role they play as vectors. The study has demonstrated the high diversity of thrips species in tomato production and the occurrence of important vectors of TSWV and other tospoviruses.

We present the first complete Australian Squash mosaic virus (SqMV) genome sequences. We compared the 2 Australian genomes from 20-year-old cucurbit samples with 8 other SqMV genomes. The Australian genomes shared >99.0% nucleotide identities, and their RNA1 and RNA2 sequences most closely resembled isolates Y and Kimbe from Japan, respectively.

We present the first complete Australian Squash mosaic virus (SqMV) genome sequences. We compared the 2 Australian genomes from 20-year-old cucurbit samples with 8 other SqMV genomes. The Australian genomes shared >99.0% nucleotide identities, and their RNA1 and RNA2 sequences most closely resembled isolates Y and Kimbe from Japan, respectively.

Analysis of an RNA-seq strand-specific library revealed a complete genome of Hardenbergia mosaic virus (HarMV) from RNA extracted from a native wisteria ( Hardenbergia comptoniana ) plant from southwest Australia. We compared it with eight other complete HarMV genomes. It most resembled (85.8% nucleotide identity) the genome of HarMV isolate MD4-D.

We present here the first complete Squash leaf curl China virus (SLCCV) genomic segment DNA-A sequence from East Timor. It was isolated from a pumpkin plant. When compared with 15 complete SLCCV DNA-A genome sequences from other world regions, it most resembled the Malaysian isolate MC1 sequence.

Analysis of an RNA-seq library from cucumber leaf RNA extracted from a fast technology for analysis of nucleic acids (FTA) card revealed the first complete genome of Cucurbit aphid-borne yellows virus (CABYV) from East Timor. We compare it with 35 complete CABYV genomes from other world regions. It most resembled the genome of the South Korean isolate HD118.

Wheat (Triticum aestivum), barley (Hordeum vulgare), and oats (Avena sativa) are some of the most economically important cereals in Australia and worldwide. Several cereal viruses are present in southeastern Australia with varied incidence and prevalence depending on year, location, and climatic conditions. Barley and cereal yellow dwarf viruses (family Luteoviridae) are increasingly prevalent in southeastern Australia (Nancarrow et al. 2018). They are transmitted by aphid vectors, mainly the bird cherry-oat aphid (Rhopalosiphum padi) and the corn leaf aphid (Rhopalosiphum maidis). High Plains wheat mosaic virus (HPWMoV) (family Fimoviridae) has been reported in Western Australia (Coutts et al. 2014), and there have been unconfirmed reports of its presence in Victoria; wheat streak mosaic virus (WSMV) (family Potyviridae) was reported in Victoria and other Australian states in 2003 (Ellis et al. 2003). Both HPWMoV and WSMV are transmitted by the wheat curl mite (Aceria tosichella) (Coutts et al. 2014). In late April 2018, a high number of R. maidis was observed on volunteer cereal plants consisting of wheat, barley, and wild oats (Avena fatua) in fields near Horsham, Victoria, Australia, together with yellowing and streaking discoloration on some plants. No evidence of wheat curl mite infestation was observed. Initially, 148 samples were collected from symptomatic and nonsymptomatic plants and tested for WSMV (DSMZ-AS0544), luteoviruses (DSMZ, AS-0227/1), and the yellow dwarf viruses BYDV-PAV, BYDV-MAV, and CYDV-RPV by tissue blot immunoassay (TBIA) (Nancarrow et al. 2018); 16 samples were positive for WSMV, 34 were positive for luteoviruses, and of the 34 luteovirus-positive samples, six were positive for at least one of the yellow dwarf viruses typically found in the Horsham region. The remaining 28 luteovirus-positive samples required further identification. In early May, a further 68 samples, prioritizing plants with streaking discoloration, were collected from the same area and tested for WSMV, luteoviruses, and HPWMoV (Agdia, SRA17200) by TBIA; 26 samples were positive for WSMV, three were positive for luteoviruses, and two were positive for HPWMoV. Two of the 216 samples tested by TBIA had mixed infections. Virus was detected in symptomatic and nonsymptomatic samples, and a number of symptomatic plants tested negative. A subset of 23 samples requiring either further identification or confirmation was additionally tested by reverse transcription polymerase chain reaction (RT-PCR) for WSMV (French and Robertson 1994), luteoviruses (Robertson et al. 1991), and HPWMoV (Lebas et al. 2005). Amplicons of the expected sizes were obtained with 11 samples positive for WSMV, 12 positive for luteoviruses, and two positive for HPWMoV. Amplicons were directly sequenced. Nucleotide sequences of the WSMV (GenBank accession MK103385) and HPWMoV (accession MK103386) amplicons were identical to accessions AY327865 (WSMV) and KT988872 (HPWMoV), respectively, confirming the presence of both viruses and hence the presence of HPWMoV in Victoria. The nucleotide sequence of the luteovirus amplicon showed 99% identity to barley virus G (BVG) (accession NC_029906). The 12 samples that tested positive for luteoviruses by TBIA and RT-PCR were further tested using two sets of BVG-specific primers (Jo et al. 2018; Park et al. 2017), each targeting a distinct region of the BVG genome; all samples were positive. An amplicon from each BVG-specific RT-PCR test was directly sequenced (accessions MK411425 and MK103388), with each showing 96% nucleotide identity to BVG (accession NC_029906), confirming the presence of BVG in these samples. Some BVG-positive samples showed yellow discoloration of the leaf tips. This is the first reported detection of BVG in Australia. BVG was reported for the first time in South Korea in 2016 (Zhao et al. 2016). Epidemiology and yield losses associated with BVG are not known in Australia or elsewhere.

We present here the first complete genomic Aphid lethal paralysis virus (ALPV) sequence isolated from cucumber plant RNA from East Timor. We compare it with two complete ALPV genome sequences from China, and one each from Israel, South Africa, and the United States. It most closely resembled the Chinese isolate LGH genome.

We present the first complete Sweet potato virus G (SPVG) genome from sweet potato in East Timor and compare it with seven complete SPVG genomes from South Korea (three), Taiwan (two), Argentina (one), and the United States (one). It most resembles the genomes from the United States and South Korea.

We present here the first complete Bean common mosaic necrosis virus (BCMNV) genomic sequence isolated from virus-infected common bean ( Phaseolus vulgaris ) in East Timor, and compare it with six complete BMCNV genomes from the Netherlands, and one each from the United States, Tanzania, and an unspecified country. It most resembled the Netherlands strain NL-8 genome.

We present here the first complete genomic RNA sequence of the polerovirus Suakwa aphid-borne yellows virus (SABYV), from East Timor. The isolate sequenced came from a virus-infected pumpkin plant. The East Timorese genome had a nucleotide identity of 86.5% with the only other SABYV genome available, which is from Taiwan.

We present here the first complete genome sequences of Sweet potato chlorotic fleck virus (SPCFV) from sweet potato in Australia and East Timor, and we compare these with four complete SPCFV genomes from South Korea and one from Uganda. The Australian, East Timorese, South Korean, and Ugandan genomes differed considerably from each other.

We present here the first complete genome sequences of Sweet potato virus 2 (SPV2) from sweet potato in Australia and East Timor, and compare these with five complete SPV2 genome sequences from South Korea and one each from Spain and the United States. Both were closely related to SPV2 genomes from South Korea, Spain, and the United States.