The complete nucleotide sequence and genome organization of pea streak virus (genus Carlavirus)

Li, Su; Li, Zhengnan; Bernardy, M. G.; Wiersma, Paul A.; Cheng, Zhihui; Yu, Xiang

doi:10.1007/s00705-015-2467-2

Cited by 7 publications

(4 citation statements)

References 6 publications

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“…Instead, it encoded a hypothetical protein of ∼6 kDa that was different from the putative nucleic-acid binding proteins of known carlaviruses. A similar genome structure was later reported for another isolate of PeSV that was 77.9% identical to the alfalfa strain of the virus at the nucleotide level and originated from an unknown host ( Su et al, 2015 ). To confirm that the genomic sequence of ALV was accurate, an infectious cDNA clone of the virus was constructed ( Nemchinov, 2017 ).…”

Section: Alfalfa Virome: Recent Developmentssupporting

confidence: 71%

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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Section: Alfalfa Virome: Recent Developmentssupporting

confidence: 71%

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

2020

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“…Phylogenetic analysis based on the amino acid sequences performed using MEGA software (Tamura et al 2011) placed this sequence in PeSV/ALV cluster close to red clover vein mosaic virus (FJ685618) (Figure 1). We propose that the sequences KP828803/AF354652 and KP784454/ AY037925 are variants of the same isolates: the first one the PeSV isolate from Wisconsin (Su et al 2015), the second one the PV-264 isolate from Nebraska (Nemchinov et al 2015). Despite different names (20) ,S→Q (26) , S→A (27) , S→T (67) amino acid substitutions concentrated on the N-terminal part of CP.…”

Section: Resultsmentioning

confidence: 99%

Pea streak virus recorded in Europe

Sarkisová¹,

Bečková²,

Fráňová³

et al. 2016

Plant Prot. Sci.

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Sarkisová T., Bečková M., Fránová J., Petrzik K. (2016): Pea streak virus recorded in Europe. Plant Protect. Sci., Alfalfa (Medicago sativa L.) is concluded to be the principal reservoir of Pea streak virus (PeSV, genus Carlavirus) which induces necrotic streaking symptoms in pea. This virus is prevalent in pea growing areas in the USA, but in Europe it was recorded only once almost 60 years ago. Recently, filamentous virus particles 600-700 nm long have been observed in examined plant sap of alfalfa with leaf malformation, local necrotic lesions and yellow spots on leaves. Four kilo base pairs nucleotide sequence of PeSV including partial replicase gene, triple gene block, and capsid protein (CP) gene has been determined. On the nucleotide level, the sequence of the CP has about 80% identity with the North American isolates of PeSV, however, on the amino acid level the sequence has more than 94% identity. This is the first sequence-based proof of PeSV presence in Europe.Keywords: carlavirus; alfalfa; Pea streak virus; partial sequence Alfalfa (Medicago sativa L.) represents one of the most important and widely planted leguminous crops. In the Czech Republic there are 18 registered cultivars growing mainly as fodder crop representing about 36% of perennial green fodder produced (Czech Statistical Office, release November 2010). Beside many fungal diseases causing the highest damage of alfalfa, there are more than 30 viruses of 15 viral families listed to be able to infect alfalfa (Brunt et al. 1996) Pea streak virus (PeSV, genus Carlavirus) was first described in 1938 (Zaumeyer 1938) and was found in pea growing areas in the USA. Alfalfa latent virus has been described in 1977 (Veerisetty & Brakke 1977), but recently it is recognised as a mild strain of PeSV causing mostly symptomless infections and distinguishable from PeSV only by typical symptoms on pea plants (Hampton 1981). PeSV is presumed to be widespread in most alfalfa growing areas (Rahman & Paeden 1993), but outside America it was recorded only once by electron microscopy and by serology in white sweet clover (Melilotus alba) in Germany (Brandes & Quantz 1957;Wetter & Quantz 1958). Only sequences of American isolates are represented in GenBank now -two identified as ALV and originated from alfalfa host, and two identified as PeSV from pea and from unknown host (Table 1). In this work we firstly describe sequence of a PeSV isolate coming from Europe. 165Plant Protect. Sci. Vol. 52, 2016, No. 3: 164-166 doi: 10.17221/157/2015-PPS MAtERiAl And MEthodsAlfalfa (Medicago sativa) plant originally designated as sample "V4" with leaves malformation (yellow spots becoming local necrotic lesion) has been found in Želešice (SE of the Czech Republic). Crude plant sap preparation from symptomatic leaves was negatively stained with uranyl acetate and inspected using transmission electron microscopy (JEM 1010; JEOL USA, Peabody, USA). RNA was isolated from the symptomatic plants with Nucleospin RNA II kit (Macherey-Nagel, Düren, Germany) according to the...

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“…Approximately 1 g of leaf tissue was used for virus and viroid double-stranded RNA (dsRNA) extraction. Extraction of dsRNA, removal of genomic DNA and single-stranded RNA (ssRNA), and construction of cDNA libraries were performed as described by Su et al [ 67 ]. The cDNA libraries were paired-end sequenced on a HiSeq 4000 platform (Illumina) by Applied Biological Materials Inc. (Richmond, BC, Canada).…”

Section: Methodsmentioning

confidence: 99%

Challenges to Cannabis sativa Production from Pathogens and Microbes—The Role of Molecular Diagnostics and Bioinformatics

Punja,

Kahl,

Reade

et al. 2023

IJMS

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The increased cultivation of Cannabis sativa L. in North America, represented by high Δ9-tetrahydrocannabinol-containing (high-THC) cannabis genotypes and low-THC-containing hemp genotypes, has been impacted by an increasing number of plant pathogens. These include fungi which destroy roots, stems, and leaves, in some cases causing a build-up of populations and mycotoxins in the inflorescences that can negatively impact quality. Viroids and viruses have also increased in prevalence and severity and can reduce plant growth and product quality. Rapid diagnosis of the occurrence and spread of these pathogens is critical. Techniques in the area of molecular diagnostics have been applied to study these pathogens in both cannabis and hemp. These include polymerase chain reaction (PCR)-based technologies, including RT-PCR, multiplex RT-PCR, RT-qPCR, and ddPCR, as well as whole-genome sequencing (NGS) and bioinformatics. In this study, examples of how these technologies have enhanced the rapidity and sensitivity of pathogen diagnosis on cannabis and hemp will be illustrated. These molecular tools have also enabled studies on the diversity and origins of specific pathogens, specifically viruses and viroids, and these will be illustrated. Comparative studies on the genomics and metabolomics of healthy and diseased plants are urgently needed to provide insight into their impact on the quality and composition of cannabis and hemp-derived products. Management of these pathogens will require monitoring of their spread and survival using the appropriate technologies to allow accurate detection, followed by appropriate implementation of disease control measures.

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The complete nucleotide sequence and genome organization of pea streak virus (genus Carlavirus)

Cited by 7 publications

References 6 publications

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

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

Pea streak virus recorded in Europe

Challenges to Cannabis sativa Production from Pathogens and Microbes—The Role of Molecular Diagnostics and Bioinformatics

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