Metagenomic Analysis Reveals a Nearly Complete Genome Sequence of
            <i>Alfalfa Mosaic Virus</i>
            from a Field Pea in Australia

Maina, Solomon; Zheng, Linda; Kinoti, Wycliff M.; Aftab, Mohammad; Nancarrow, Narelle; Trębicki, Piotr; King, Simon; Constable, Fiona; Rodoni, Brendan

doi:10.1128/mra.00766-19

Cited by 10 publications

(8 citation statements)

References 15 publications

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“…In phylogenetic analyses of RNAs 1, 2, and 3, AMV-AU formed a tight cluster with cognate AMV genome sequences deposited in GenBank (data not shown), similar to an earlier CP sequence phylogenetic analysis of Australian and global AMV isolates [45]. Nucleotide sequence identities between the Victorian AMV isolates from alfalfa and field pea [48] were 99.1%, 94.7%, and 99.3% for RNAs 1, 2 and 3, respectively (Table S2). Sequence identities of both nt and deduced amino acid (aa) sequences for Protein 1 (P1), Protein 2 (P2), Movement Protein (MP), and CP genes ranged from 94.2% to 100% (Table S2).…”

Section: Genome Assembly and Sequence Comparisons Of Amv And Blrv Isosupporting

confidence: 82%

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

Samarfard

McTaggart

Sharman³

et al. 2020

Pathogens

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Alfalfa plants in the field can display a range of virus-like symptoms, especially when grown over many years for seed production. Most known alfalfa viruses have RNA genomes, some of which can be detected using diagnostic assays, but many viruses of alfalfa are not well characterized. This study aims to identify the RNA and DNA virus complexes associated with alfalfa plants in Australia. To maximize the detection of RNA viruses, we purified double-stranded RNA (dsRNA) for high throughput sequencing and characterized the viromes of ten alfalfa samples that showed diverse virus-like symptoms. Using Illumina sequencing of tagged cDNA libraries from immune-captured dsRNA, we identified sequences of the single-stranded RNA viruses, alfalfa mosaic virus (AMV), bean leafroll virus, a new emaravirus tentatively named alfalfa ringspot-associated virus, and persistent dsRNA viruses belonging to the families Amalgaviridae and Partitiviridae. Furthermore, rolling circle amplification and restriction enzyme digestion revealed the complete genome of chickpea chlorosis Australia virus, a mastrevirus (family Geminiviridae) previously reported only from chickpea and French bean that was 97% identical to the chickpea isolate. The sequence data also enabled the assembly of the first complete genome (RNAs 1–3) of an Australian AMV isolate from alfalfa.

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Section: Genome Assembly and Sequence Comparisons Of Amv And Blrv Isosupporting

confidence: 82%

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

Samarfard

McTaggart

Sharman³

et al. 2020

Pathogens

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“…AMV can be transmitted by several aphid species in a nonpersistent manner, and also by mechanical inoculation, seed and pollen of some plants ( Edwardson and Christie, 1997 ; He et al, 2010 ; Hiruki and Hampton, 1990 ). AMV was first isolated from alfalfa ( Medicago sativa ) in the United States in 1931 ( Weimer, 1931 ) and to date, it has occurred in several countries (including Australia, New Zealand, Saudi Arabia, North and South America, France, England, Italy, Greece, Egypt, China, and Iran) with the various degree of economic losses ( Al-Shahwan, 2002 ; Che et al, 2020 ; Fletcher, 2001 ; Maina et al, 2019 ; Massumi et al, 2012 ; Sawalha and Mansour, 1996 ). This virus can naturally infect 698 species of 167 genera in 71 families ( Edwardson and Christie 1997 ; Fletcher, 2001 ; Jasper and Bos, 1980 ; Xu and Nie, 2006 ).…”

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confidence: 99%

Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of Vinca minor and Wisteria sinensis in Iran: with Implications for the Genetic Structure of the Virus

Moradi

Mehrvar

2021

Plant Pathol J

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Alfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De novo assembly and annotating of contigs revealed that RNA1, RNA2, and RNA3 genomic fragments consist of 3,690, 2,636, and 2,057 nucleotides (nt) for IR-VM and 3,690, 2,594, and 2,057 nt for IR-WS. RNA1 and RNA3 segments of IR-VM and IR-WS closely resembled those of the Chinese isolate HZ, with 99.23-99.26% and 98.04-98.09% nt identity, respectively. Their RNA2 resembled that of Canadian isolate CaM and American isolate OH-2-2017, with 97.96-98.07% nt identity. The P2 gene revealed more nucleotide diversity compared with other genes. Genes in the AMV genome were under dominant negative selection during evolution, and the P1 and coat protein (CP) proteins were subject to the strongest and weakest purifying selection, respectively. In the population genetic analysis based on the CP gene sequences, all 107 AMV isolates fell into two main clades (A, B) and isolates of clade A were further divided into three groups with significant subpopulation differentiation. The results indicated moderate genetic variation within and no clear geographic or genetic structure between the studied populations, implying moderate gene flow can play an important role in differentiation and distribution of genetic diversity among populations. Several factors have shaped the genetic structure and diversity of AMV: selection, recombination/reassortment, gene flow, and random processes such as founder effects.

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“…Alfalfa mosaic virus (AMV) is one of the most important plant viruses distributed worldwide, with a very broad host range ( Maina et al, 2019 ). Despite the large amount of data accumulated on AMV, the application of HTS was necessary to obtain the first complete nucleotide sequence of AMV isolated from alfalfa as a natural host ( Trucco et al, 2014 ).…”

Section: Alfalfa Virome: Recent Developmentsmentioning

confidence: 99%

High-Throughput Sequencing for Deciphering the Virome of Alfalfa (Medicago sativa L.)

2020

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Alfalfa ( Medicago sativa L.), also known as lucerne, is a major forage crop worldwide. In the United States, it has recently become the third most valuable field crop, with an estimated value of over $9.3 billion. Alfalfa is naturally infected by many different pathogens, including viruses, obligate parasites that reproduce only inside living host cells. Traditionally, viral infections of alfalfa have been considered by breeders, growers, producers and researchers to be diseases of limited importance, although they are widespread in all major cultivation areas. However, over the past few years, due to the rapid development of high-throughput sequencing (HTS), viral metagenomics, bioinformatics tools for interpreting massive amounts of HTS data and the increasing accessibility of public data repositories for transcriptomic discoveries, several emerging viruses of alfalfa with the potential to cause serious yield losses have been described. They include alfalfa leaf curl virus (family Geminiviridae ), alfalfa dwarf virus (family Rhabdoviridae ), alfalfa enamovirus 1 (family Luteoviridae ), alfalfa virus S (family Alphaflexiviridae ) and others. These discoveries have called into question the assumed low economic impact of viral diseases in alfalfa and further suggested their possible contribution to the severity of complex infections involving multiple pathogens. In this review, we will focus on viruses of alfalfa recently described in different laboratories on the basis of the above research methodologies.

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Metagenomic Analysis Reveals a Nearly Complete Genome Sequence of Alfalfa Mosaic Virus from a Field Pea in Australia

Cited by 10 publications

References 15 publications

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of Vinca minor and Wisteria sinensis in Iran: with Implications for the Genetic Structure of the Virus

High-Throughput Sequencing for Deciphering the Virome of Alfalfa (Medicago sativa L.)

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