Novel mastreviruses identified in Australian wild rice

Kraberger, Simona; Geering, Andrew D. W.; Walters, Matthew; Martin, Darren P.; Varsani, Arvind

doi:10.1016/j.virusres.2017.07.003

Cited by 14 publications

(7 citation statements)

References 31 publications

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“…NGS applications in plant virology began in 2009 (Blawid, Silva and Nagata, 2017) and have been increasingly applied in the de novo discovery of RNA and DNA viruses as well as viroids due to its rise as a rapid and relatively inexpensive mode of viral detection (Hadidi et al 2016; Blawid, Silva and Nagata, 2017). Previous reports of using NGS for novel viral discovery and subsequent evolutionary analysis are well-documented (Kehoe et al 2014; Alicai et al 2016; Ndunguru et al 2015; Wamonje et al 2017; Maina et al 2017; Kraberger et al 2017). In this study, we use this approach to obtain near complete genomes of BCMNV and CABMV, and gain further insights into the evolutionary relationships of BCMNV and CABMV.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary insights into Bean common mosaic necrosis virus and Cowpea aphid borne mosaic virus using global isolates and thirteen new near complete genomes from Kenya

Wainaina

Kubatko

Harvey

et al. 2018

Preprint

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Plant viral diseases are one of the major limitations in legume production within sub Saharan Africa (SSA), as they account for up to 100 % in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out. The main aim was to gain insights into the selection pressure and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV), within symptomatic common beans and cowpeas. Eleven near complete genomes of BCMNV and two for CABMV sequences were obtained from SSA. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes was carried out. Three distinct well-supported clades were identified across the whole genome tree, and were in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. These results will contribute greatly to the knowledge gap surrounding the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and support the current breeding efforts towards resistance for BCMNV and CABMV.

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Section: Introductionmentioning

confidence: 99%

Evolutionary insights into Bean common mosaic necrosis virus and Cowpea aphid borne mosaic virus using global isolates and thirteen new near complete genomes from Kenya

Wainaina

Kubatko

Harvey

et al. 2018

Preprint

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“…In addition, Tables 2 and 3 show that, currently, there are no viruses recorded infecting rice in Australia. However, two mastreviruses named rice latent viruses 1 and 2 were found in infecting wild rice species in the Cape York Peninsula in tropical northern QLD [67] so this likely reflects lack of attention paid by virologists and rice farmers rather than their complete absence. Similarly, there are no records of virus infection in linseed.…”

Section: Viruses Infecting Cereal and Oilseed Cropsmentioning

confidence: 99%

Virus Diseases of Cereal and Oilseed Crops in Australia: Current Position and Future Challenges

Jones

Sharman

Trębicki

et al. 2021

Viruses

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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.

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“…However, many of the divergent members of the family (including most of the unclassified species) have been identified in non-cultivated native plants. In some instances, plants showed no observable visual symptoms, or only very mild symptoms caused by the virus [15,27,33,[39][40][41]. The native and non-cultivated plants within which these divergent geminiviruses occur can act as reservoirs for viral species with the potential to emerge as crop pathogens [42,43].…”

Section: Introductionmentioning

confidence: 99%

New World Cactaceae Plants Harbor Diverse Geminiviruses

Fontenele

Salywon

Majure

et al. 2021

Viruses

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The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infects them. We previously identified a highly divergent geminivirus that is the first known to infect cacti. Recent research efforts in non-cultivated and asymptomatic plants have shown that the diversity of this viral family has been under-sampled. As a consequence, little is known about the effects and interactions of geminiviruses in many plants, such as cacti. With the objective to expand knowledge on the diversity of geminiviruses infecting cacti, we used previously acquired high-throughput sequencing results to search for viral sequences using BLASTx against a viral RefSeq protein database. We identified two additional sequences with similarity to geminiviruses, for which we designed abutting primers and recovered full-length genomes. From 42 cacti and five scale insects, we derived 42 complete genome sequences of a novel geminivirus species that we have tentatively named Opuntia virus 2 (OpV2) and 32 genomes of an Opuntia-infecting becurtovirus (which is a new strain of the spinach curly top Arizona virus species). Interspecies recombination analysis of the OpV2 group revealed several recombinant regions, in some cases spanning half of the genome. Phylogenetic analysis demonstrated that OpV2 is a novel geminivirus more closely related to viruses of the genus Curtovirus, which was further supported by the detection of three recombination events between curtoviruses and OpV2. Both OpV2 and Opuntia becurtoviruses were identified in mixed infections, which also included the previously characterized Opuntia virus 1. Viral quantification of the co-infected cactus plants compared with single infections did not show any clear trend in viral dynamics that might be associated with the mixed infections. Using experimental Rhizobium-mediated inoculations, we found that the initial accumulation of OpV2 is facilitated by co-infection with OpV1. This study shows that the diversity of geminiviruses that infect cacti is under-sampled and that cacti harbor diverse geminiviruses. The detection of the Opuntia becurtoviruses suggests spill-over events between viruses of cultivated species and native vegetation. The threat this poses to cacti needs to be further investigated.

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Novel mastreviruses identified in Australian wild rice

Abstract: 156 words Text: 1674 wordsFigures: 2 AbstractMost known mastreviruses (family Geminiviridae) infect members of the grass family, Poaceae.

Cited by 14 publications

References 31 publications

Evolutionary insights into Bean common mosaic necrosis virus and Cowpea aphid borne mosaic virus using global isolates and thirteen new near complete genomes from Kenya

Evolutionary insights into Bean common mosaic necrosis virus and Cowpea aphid borne mosaic virus using global isolates and thirteen new near complete genomes from Kenya

Virus Diseases of Cereal and Oilseed Crops in Australia: Current Position and Future Challenges

New World Cactaceae Plants Harbor Diverse Geminiviruses

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