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Article ; Online: Complete genome sequence of alfalfa-associated picorna-like virus 2.

Nemchinov, Lev G / Grinstead, Sam

Microbiology resource announcements

2024 Volume 13, Issue 4, Page(s) e0105223

Abstract: We have previously reported on the detection of an unknown picorna-like virus in alfalfa samples. The exact host of the virus was unclear due to its similarity to the members ... ...

Abstract	We have previously reported on the detection of an unknown picorna-like virus in alfalfa samples. The exact host of the virus was unclear due to its similarity to the members of
Language	English
Publishing date	2024-03-01
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/mra.01052-23
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Article ; Online: Genome-wide identification of endogenous viral sequences in alfalfa (Medicago sativa L.).

Boutanaev, Alexander M / Nemchinov, Lev G

Virology journal

2021 Volume 18, Issue 1, Page(s) 185

Abstract: Endogenous viral elements (EVEs) have been for the most part described in animals and to a less extent in plants. The endogenization was proposed to contribute toward evolution of living organisms via horizontal gene transfer of novel genetic material ... ...

Abstract	Endogenous viral elements (EVEs) have been for the most part described in animals and to a less extent in plants. The endogenization was proposed to contribute toward evolution of living organisms via horizontal gene transfer of novel genetic material and resultant genetic diversity. During the last two decades, several full-length and fragmented EVEs of pararetroviral and non-retroviral nature have been identified in different plant genomes, both monocots and eudicots. Prior to this work, no EVEs have been reported in alfalfa (Medicago sativa L.), the most cultivated forage legume in the world. In this study, taking advantage of the most recent developments in the field of alfalfa research, we have assessed alfalfa genome on the presence of viral-related sequences. Our analysis revealed segmented EVEs resembling two dsDNA reverse-transcribing virus species: Soybean chlorotic mottle virus (family Caulimoviridae, genus Soymovirus) and Figwort mosaic virus (family Caulimoviridae, genus Caulimovirus). The EVEs appear to be stable constituents of the host genome and in that capacity could potentially acquire functional roles in alfalfa's development and response to environmental stresses.
MeSH term(s)	Caulimoviridae/genetics ; Caulimovirus/genetics ; Genome, Plant ; Medicago sativa/genetics ; Medicago sativa/virology
Language	English
Publishing date	2021-09-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2160640-7
ISSN	1743-422X ; 1743-422X
ISSN (online)	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-021-01650-9
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Article ; Online: Snake River alfalfa virus, a persistent virus infecting alfalfa (Medicago sativa L.) in Washington State, USA.

Postnikova, Olga A / Irish, Brian M / Eisenback, Jonathan / Nemchinov, Lev G

Virology journal

2023 Volume 20, Issue 1, Page(s) 32

Abstract: Here we report an occurrence of Snake River alfalfa virus (SRAV) in Washington state, USA. SRAV was recently identified in alfalfa (Medicago sativa L.) plants and western flower thrips in south-central Idaho and proposed to be a first flavi-like virus ... ...

Abstract	Here we report an occurrence of Snake River alfalfa virus (SRAV) in Washington state, USA. SRAV was recently identified in alfalfa (Medicago sativa L.) plants and western flower thrips in south-central Idaho and proposed to be a first flavi-like virus identified in a plant host. We argue that the SRAV, based on its prevalence in alfalfa plants, readily detectable dsRNA, genome structure, presence in alfalfa seeds, and seed-mediated transmission is a persistent new virus distantly resembling members of the family Endornaviridae.
MeSH term(s)	Medicago sativa ; Washington ; Rivers ; Seeds
Language	English
Publishing date	2023-02-19
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2160640-7
ISSN	1743-422X ; 1743-422X
ISSN (online)	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-023-01991-7
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Article ; Online: Characterization of the seed virome of alfalfa (Medicago sativa L).

Nemchinov, Lev G / Irish, Brian M / Grinstead, Sam / Postnikova, Olga A

Virology journal

2023 Volume 20, Issue 1, Page(s) 96

Abstract: Background: Seed transmission of plant viruses can be important due to the role it plays in their dissemination to new areas and subsequent epidemics. Seed transmission largely depends on the ability of a virus to replicate in reproductive tissues and ... ...

Abstract	Background: Seed transmission of plant viruses can be important due to the role it plays in their dissemination to new areas and subsequent epidemics. Seed transmission largely depends on the ability of a virus to replicate in reproductive tissues and survive during the seed maturation process. It occurs through the infected embryo or mechanically through the contaminated seed coat. Alfalfa (Medicago sativa L.) is an important legume forage crop worldwide, and except for a few individual seedborne viruses infecting the crop, its seed virome is poorly known. The goal of this research was to perform initial seed screenings on alfalfa germplasm accessions maintained by the USDA ARS National Plant Germplasm System in order to identify pathogenic viruses and understand their potential for dissemination. Methods: For the detection of viruses, we used high throughput sequencing combined with bioinformatic tools and reverse transcription-polymerase chain reactions. Results: Our results suggest that, in addition to common viruses, alfalfa seeds are infected by other potentially pathogenic viral species that could be vertically transmitted to offspring. Conclusions: To the best of our knowledge, this is the first study of the alfalfa seed virome carried out by HTS technology. This initial screening of alfalfa germplasm accessions maintained by the NPGS showed that the crop's mature seeds contain a broad range of viruses, some of which were not previously considered to be seed-transmitted. The information gathered will be used to update germplasm distribution policies and to make decisions on the safety of distributing germplasm based on viral presence.
MeSH term(s)	Medicago sativa ; Virome ; Computational Biology ; Seeds ; Plant Viruses/genetics
Language	English
Publishing date	2023-05-19
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2160640-7
ISSN	1743-422X ; 1743-422X
ISSN (online)	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-023-02063-6
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Article: An Expansin-Like Candidate Effector Protein from

Vieira, Paulo / Nemchinov, Lev G

Phytopathology

2020 Volume 110, Issue 3, Page(s) 684–693

Abstract: The root lesion nematode (RLN) ...

Abstract	The root lesion nematode (RLN)
MeSH term(s)	Animals ; Helminth Proteins ; Plant Diseases ; Plant Roots ; Nicotiana ; Tylenchoidea
Chemical Substances	Helminth Proteins
Language	English
Publishing date	2020-01-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	208889-7
ISSN	1943-7684 ; 0031-949X
ISSN (online)	1943-7684
ISSN	0031-949X
DOI	10.1094/PHYTO-09-19-0336-R
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Article: Identification of a Novel Isolate of

Nemchinov, Lev G / Grinstead, Samuel

Plant disease

2020 Volume 104, Issue 12, Page(s) 3115–3117

Abstract: Recently, alfalfa virus S (AVS), a new species in the ... ...

Abstract	Recently, alfalfa virus S (AVS), a new species in the family
MeSH term(s)	China ; Flexiviridae ; Medicago sativa ; Role ; Seeds ; Sudan
Language	English
Publishing date	2020-10-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	754182-x
ISSN	0191-2917
ISSN	0191-2917
DOI	10.1094/PDIS-04-20-0906-SC
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Article: An Expansin-Like Candidate Effector Protein from Pratylenchus penetrans Modulates Immune Responses in Nicotiana benthamiana

Vieira, Paulo / Nemchinov, Lev G

Phytopathology. 2020 Mar., v. 110, no. 3

2020

Abstract: The root lesion nematode (RLN) Pratylenchus penetrans is a migratory species that attacks a broad range of crops. After the RLN is initially attracted to host roots by root exudates and compounds, it releases secretions that are critical for successful ... ...

Abstract	The root lesion nematode (RLN) Pratylenchus penetrans is a migratory species that attacks a broad range of crops. After the RLN is initially attracted to host roots by root exudates and compounds, it releases secretions that are critical for successful parasitism. Among those secretions are nematode virulence factors or effectors that facilitate the entry and migration of nematodes through the roots and modulate plant immune defenses. The recognition of the effectors by host resistance proteins leads to effector-triggered immunity and incompatible plant–nematode interactions. Although many candidate effectors of the RLN and other plant-parasitic nematodes have been identified, the detailed mechanisms of their functions and particularly, their host targets remain largely unexplored. In this study, we sequenced and annotated genes encoding expansin-like proteins, which are major candidate effectors of P. penetrans. One of the genes, Pp-EXPB1, which was the most highly expressed during nematode infection in different plant species, was further functionally characterized via transient expression in the model plant Nicotiana benthamiana and global transcriptome profiling of gene expression changes triggered by this candidate effector in plants. As a result of this investigation, the biological roles of Pp-EXPB1 in nematode parasitism were proposed, the putative cellular targets of the proteins were identified, and the molecular mechanisms of plant responses to the nematode-secreted proteins were outlined.
Keywords	crops ; gene expression ; genes ; immune response ; migratory species ; models ; nematode infections ; Nicotiana benthamiana ; parasitism ; plant response ; Pratylenchus penetrans ; proteins ; root exudates ; root lesion nematodes ; roots ; secretion ; transcriptomics ; virulence
Language	English
Dates of publication	2020-03
Size	p. 684-693.
Publishing place	Phytopathology
Document type	Article
ZDB-ID	208889-7
ISSN	1943-7684 ; 0031-949X
ISSN (online)	1943-7684
ISSN	0031-949X
DOI	10.1094/PHYTO-09-19-0336-R
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Article ; Online: Characterization of the seed virome of alfalfa (Medicago sativa L)

Nemchinov, Lev G. / Irish, Brian M. / Grinstead, Sam / Postnikova, Olga A.

Virology Journal. 2023 May 19, v. 20, no. 1 p.96-

2023

Abstract	Background: Seed transmission of plant viruses can be important due to the role it plays in their dissemination to new areas and subsequent epidemics. Seed transmission largely depends on the ability of a virus to replicate in reproductive tissues and survive during the seed maturation process. It occurs through the infected embryo or mechanically through the contaminated seed coat. Alfalfa (Medicago sativa L.) is an important legume forage crop worldwide, and except for a few individual seedborne viruses infecting the crop, its seed virome is poorly known. The goal of this research was to perform initial seed screenings on alfalfa germplasm accessions maintained by the USDA ARS National Plant Germplasm System in order to identify pathogenic viruses and understand their potential for dissemination. Methods: For the detection of viruses, we used high throughput sequencing combined with bioinformatic tools and reverse transcription-polymerase chain reactions. Results: Our results suggest that, in addition to common viruses, alfalfa seeds are infected by other potentially pathogenic viral species that could be vertically transmitted to offspring. Conclusions: To the best of our knowledge, this is the first study of the alfalfa seed virome carried out by HTS technology. This initial screening of alfalfa germplasm accessions maintained by the
Keywords	Medicago sativa ; USDA National Plant Germplasm System ; alfalfa ; bioinformatics ; forage crops ; germplasm ; progeny ; seed coat ; seed maturation ; virology ; viruses
Language	English
Dates of publication	2023-0519
Publishing place	Springer Science and Business Media LLC
Document type	Article ; Online
Note	Resource is Open Access
ZDB-ID	2160640-7
ISSN	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-023-02063-6
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Snake River alfalfa virus, a persistent virus infecting alfalfa (Medicago sativa L.) in Washington State, USA

Postnikova, Olga A. / Irish, Brian M. / Eisenback, Jonathan / Nemchinov, Lev G.

Virol J. 2023 Dec., v. 20, no. 1 p.32-32

2023

Abstract	Here we report an occurrence of Snake River alfalfa virus (SRAV) in Washington state, USA. SRAV was recently identified in alfalfa (Medicago sativa L.) plants and western flower thrips in south-central Idaho and proposed to be a first flavi-like virus identified in a plant host. We argue that the SRAV, based on its prevalence in alfalfa plants, readily detectable dsRNA, genome structure, presence in alfalfa seeds, and seed-mediated transmission is a persistent new virus distantly resembling members of the family Endornaviridae.
Keywords	Endornaviridae ; Frankliniella occidentalis ; Medicago sativa ; Washington (state) ; alfalfa ; genome ; host plants ; viruses ; Idaho ; Snake River
Language	English
Dates of publication	2023-12
Size	p. 32.
Publishing place	BioMed Central
Document type	Article ; Online
ZDB-ID	2160640-7
ISSN	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-023-01991-7
Database	NAL-Catalogue (AGRICOLA)

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Article: Genome-wide identification of endogenous viral sequences in alfalfa (Medicago sativa L.)

Boutanaev, Alexander M. / Nemchinov, Lev G.

Virology journal. 2021 Dec., v. 18, no. 1

2021

Abstract	Endogenous viral elements (EVEs) have been for the most part described in animals and to a less extent in plants. The endogenization was proposed to contribute toward evolution of living organisms via horizontal gene transfer of novel genetic material and resultant genetic diversity. During the last two decades, several full-length and fragmented EVEs of pararetroviral and non-retroviral nature have been identified in different plant genomes, both monocots and eudicots. Prior to this work, no EVEs have been reported in alfalfa (Medicago sativa L.), the most cultivated forage legume in the world. In this study, taking advantage of the most recent developments in the field of alfalfa research, we have assessed alfalfa genome on the presence of viral-related sequences. Our analysis revealed segmented EVEs resembling two dsDNA reverse-transcribing virus species: Soybean chlorotic mottle virus (family Caulimoviridae, genus Soymovirus) and Figwort mosaic virus (family Caulimoviridae, genus Caulimovirus). The EVEs appear to be stable constituents of the host genome and in that capacity could potentially acquire functional roles in alfalfa’s development and response to environmental stresses.
Keywords	DNA ; Figwort mosaic virus ; Liliopsida ; Medicago sativa ; Soybean chlorotic mottle virus ; alfalfa ; evolution ; forage legumes ; genetic variation ; genome ; horizontal gene transfer ; virology ; viruses
Language	English
Dates of publication	2021-12
Size	p. 185.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2160640-7
ISSN	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-021-01650-9
Database	NAL-Catalogue (AGRICOLA)

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