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Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

Importance: Globally, viral diseases impair the growth and vigor of cultivated crops such as grains, leading to a significant reduction in quality, marketability, and competitiveness. As an island nation, Australia has a distinct advantage in using its border to prevent the introduction of damaging viruses, which threaten the continental agricultural sector. However, breeding programs in Australia rely on imported seeds as new sources of genetic diversity. As such, it is critical to remain vigilant in identifying new and emerging viral pathogens, by ensuring the availability of accurate genomic diagnostic tools at the grain biosecurity border. High-throughput sequencing offers game-changing opportunities in biosecurity routine testing. Genomic results are more accurate and informative compared to traditional molecular methods or biological indexing. The present work contributes to strengthening accurate phytosanitary screening, to safeguard the Australian grains industry, and expedite germplasm release to the end users., Competing Interests: The authors declare no conflict of interest.

This review summarizes research on virus diseases of cereals and oilseeds in Australia since the 1950s. All viruses known to infect the diverse range of cereal and oilseed crops grown in the continent's temperate, Mediterranean, subtropical and tropical cropping regions are included. Viruses that occur commonly and have potential to cause the greatest seed yield and quality losses are described in detail, focusing on their biology, epidemiology and management. These are: barley yellow dwarf virus, cereal yellow dwarf virus and wheat streak mosaic virus in wheat, barley, oats, triticale and rye; Johnsongrass mosaic virus in sorghum, maize, sweet corn and pearl millet; turnip yellows virus and turnip mosaic virus in canola and Indian mustard; tobacco streak virus in sunflower; and cotton bunchy top virus in cotton. The currently less important viruses covered number nine infecting nine cereal crops and 14 infecting eight oilseed crops (none recorded for rice or linseed). Brief background information on the scope of the Australian cereal and oilseed industries, virus epidemiology and management and yield loss quantification is provided. Major future threats to managing virus diseases effectively include damaging viruses and virus vector species spreading from elsewhere, the increasing spectrum of insecticide resistance in insect and mite vectors, resistance-breaking virus strains, changes in epidemiology, virus and vectors impacts arising from climate instability and extreme weather events, and insufficient industry awareness of virus diseases. The pressing need for more resources to focus on addressing these threats is emphasized and recommendations over future research priorities provided.

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., (© 2021 The Authors. Published by Elsevier B.V.)

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.

Background: The 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., Results: We 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., Conclusions: The 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., (© The Author(s) 2019. Published by Oxford University Press.)

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., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

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.

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.

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

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.

Background: Maize lethal necrosis is caused by a synergistic co-infection of Maize chlorotic mottle virus (MCMV) and a specific member of the Potyviridae, such as Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) or Johnson grass mosaic virus (JGMV). Typical maize lethal necrosis symptoms include severe yellowing and leaf drying from the edges. In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA., Methods: We used next-generation sequencing to identify viruses associated to maize lethal necrosis in Kenya through a metagenomics analysis. Symptomatic and asymptomatic leaf samples were collected from maize and sorghum representing sixteen counties., Results: Complete and partial genomes were assembled for MCMV, SCMV, Maize streak virus (MSV) and Maize yellow dwarf virus-RMV (MYDV-RMV). These four viruses (MCMV, SCMV, MSV and MYDV-RMV) were found together in 30 of 68 samples. A geographic analysis showed that these viruses are widely distributed in Kenya. Phylogenetic analyses of nucleotide sequences showed that MCMV, MYDV-RMV and MSV are similar to isolates from East Africa and other parts of the world. Single nucleotide polymorphism, nucleotide and polyprotein sequence alignments identified three genetically distinct groups of SCMV in Kenya. Variation mapped to sequences at the border of NIb and the coat protein. Partial genome sequences were obtained for other four potyviruses and one polerovirus., Conclusion: Our results uncover the complexity of the maize lethal necrosis epidemic in Kenya. MCMV, SCMV, MSV and MYDV-RMV are widely distributed and infect both maize and sorghum. SCMV population in Kenya is diverse and consists of numerous strains that are genetically different to isolates from other parts of the world. Several potyviruses, and possibly poleroviruses, are also involved.

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 PVS A and PVS O , respectively. When nine wild potato species were inoculated, most developed symptomless systemic infection but Solanum megistacrolobum developed systemic hypersensitive resistance (SHR) with one PVS O and two PVS A isolates. Andean potato cultivars developed mostly asymptomatic primary infection but predominantly symptomatic secondary infection. In both wild and cultivated potato plants, PVS A and PVS O elicited similar foliage symptoms. Following graft inoculation, all except two PVS O isolates were detected in partially PVS-resistant cultivar Saco, while clone Snec 66/139-19 developed SHR with two isolates each of PVS A and PVS O . Myzus persicae transmitted all nine PVS A isolates but none of the three PVS O 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 PVS A isolates but less than 21 days for the three PVS O isolates. Dilution end points were 10 -3 for two PVS O 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.

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., (Copyright © 2018 Maina et al.)

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.

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., (Copyright © 2017 Maina et al.)

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., (Copyright © 2017 Maina and Jones.)

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.

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., (Copyright © 2017 Maina et al.)

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.

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., (Copyright © 2017 Maina et al.)

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.

Brachiaria grass is an emerging forage option for livestock production in Kenya. Kenya lies within the center of diversity for Brachiaria species, thus a high genetic variation in natural populations of Brachiaria is expected. Overgrazing and clearing of natural vegetation for crop production and nonagricultural uses and climate change continue to threaten the natural biodiversity. In this study, we collected 79 Brachiaria ecotypes from different parts of Kenya and examined them for genetic variations and their relatedness with 8 commercial varieties. A total of 120 different alleles were detected by 22 markers in the 79 ecotypes. Markers were highly informative in differentiating ecotypes with average diversity and polymorphic information content of 0.623 and 0.583, respectively. Five subpopulations: International Livestock Research Institute (ILRI), Kitui, Kisii, Alupe, and Kiminini differed in sample size, number of alleles, number of private alleles, diversity index, and percentage polymorphic loci. The contribution of within-the-individual difference to total genetic variation of Kenyan ecotype population was 81%, and the fixation index ( F ST = 0.021) and number of migrant per generation ( N m = 11.58) showed low genetic differentiation among the populations. The genetic distance was highest between Alupe and Kisii populations (0.510) and the lowest between ILRI and Kiminini populations (0.307). The unweighted neighbor-joining (NJ) tree showed test ecotypes grouped into three major clusters: ILRI ecotypes were present in all clusters; Kisii and Alupe ecotypes and improved varieties grouped in clusters I and II; and ecotypes from Kitui and Kiminini grouped in cluster I. This study confirms higher genetic diversity in Kenyan ecotypes than eight commercial varieties (Basilisk, Humidicola, Llanero, Marandú, MG4, Mulato II, Piatá and Xaraés) that represent three species and one three-way cross-hybrid Mulato II. There is a need for further collection of local ecotypes and their morphological, agronomical, and genetic characterizations to support Brachiaria grass breeding and conservation programs., (© 2017 by the authors.)

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., (Copyright © 2017 Maina et al.)

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., (Copyright © 2016 Maina et al.)

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., (Copyright © 2016 Maina et al.)

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., (Copyright © 2016 Maina et al.)

Background: Multiple types of solid waste in developing countries is disposed of together in dumpsites where there is interaction between humans, animals and the bacteria in the waste. To study the bacteria at the dumpsite and the associated risks, previous studies have focused on culturable, leaving behind a great number of unculturable bacteria. This study focuses on a more comprehensive approach to study bacteria at the dumpsite. Since the site comprised of unsorted wastes, a qualitative survey was first performed to identify the variety of solid waste as this has influence on the microbial composition. Thus, domestic (Dom), biomedical (Biom), river sludge (Riv), and fecal material of pigs scavenging on the dumpsite (FecD) were sampled. Total DNA was extracted from 78 samples and the v4-16S rRNA amplicons was characterized using an Illumina MiSeq platform., Results: A total of 8,469,294 sequences passed quality control. Catchall analysis predicted a mean of 8243 species per sample. Diversity was high with an average InvSimpson index of 44.21 ± 1.44. A total of 35 phyla were detected and the predominant were Firmicutes (38 %), Proteobacteria (35 %), Bacteroidetes (13 %) and Actinobacteria (3 %). Overall 76,862 OTUs were detected, however, only 20 % were found more than 10 times. The predominant OTUs were Acinetobacter (12.1 %), Clostridium sensu stricto (4.8 %), Proteinclasticum and Lactobacillus both at (3.4 %), Enterococcus (2.9 %) and Escherichia/Shigella (1.7 %). Indicator analysis (P ≤ 0.05, indicator value ≥ 70) shows that Halomonas, Idiomarina, Tisierella and Proteiniclasticum were associated with Biom; Enterococcus, Bifidobacteria, and Clostridium sensu stricto with FecD and Flavobacteria, Lysobacter and Commamonas to Riv. Acinetobacter and Clostridium sensu stricto were found in 62 % and 49 % of all samples, respectively, at the relative abundance of 1 %. None of OTUs was found across all samples., Conclusions: This study provides a comprehensive report on the abundance and diversity bacteria in municipal dumpsite. The species richness reported here shows the complexity of this man-made ecosystem and calls for further research to assess for a link between human diseases and the dumpsite. This would provide insight into proper disposal of the waste, as well as, limit the risks to human health associated with the dumpsite.

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., (Copyright © 2016 Maina et al.)

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., (Copyright © 2016 Maina et al.)

We present here the first complete genomic RNA sequence of the polerovirus Pepper vein yellows virus (PeVYV) obtained from a pepper plant in Australia. We compare it with complete PeVYV genomes from Japan and China. The Australian genome was more closely related to the Japanese than the Chinese genome., (Copyright © 2016 Maina et al.)

Cassava brown streak disease is caused by two devastating viruses, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) which are frequently found infecting cassava, one of sub-Saharan Africa's most important staple food crops. Each year these viruses cause losses of up to $100 million USD and can leave entire families without their primary food source, for an entire year. Twelve new whole genomes, including seven of CBSV and five of UCBSV were uncovered in this research, doubling the genomic sequences available in the public domain for these viruses. These new sequences disprove the assumption that the viruses are limited by agro-ecological zones, show that current diagnostic primers are insufficient to provide confident diagnosis of these viruses and give rise to the possibility that there may be as many as four distinct species of virus. Utilizing NGS sequencing technologies and proper phylogenetic practices will rapidly increase the solution to sustainable cassava production.

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., (© The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)