Academic Journal
Προβολή σε EDS

Characterization of yam virus X isolates from Dioscorea trifida in Brazil.

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος: Characterization of yam virus X isolates from Dioscorea trifida in Brazil.
Συγγραφείς: Araújo CPFS; Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7B, 38124, Brunswick, Germany., Knierim D; Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7B, 38124, Brunswick, Germany., de Oliveira SAS; Embrapa Mandioca e Fruticultura, Rua Embrapa S/nº, Chapadinha, Bahia, 44380-000, Cruz das Almas, Brazil., Blawid R; Department of Agronomy, Federal Rural University of Pernambuco, Rua Dom Manuel de Medeiros S/nº, Dois Irmãos, Pernambuco, 52171-900, Recife, Brazil., Margaria P; Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7B, 38124, Brunswick, Germany. paolo.margaria@dsmz.de.
Πηγή: BMC research notes [BMC Res Notes] 2026 Sep 02; Vol. 19 (1). Date of Electronic Publication: 2026 Sep 02.
Τύπος έκδοσης: Journal Article
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Biomed Central Country of Publication: England NLM ID: 101462768 Publication Model: Electronic Cited Medium: Internet ISSN: 1756-0500 (Electronic) Linking ISSN: 17560500 NLM ISO Abbreviation: BMC Res Notes Subsets: MEDLINE
Imprint Name(s): Original Publication: London : Biomed Central, 2008.
Ιατρικοί όροι (MeSH): Dioscorea*/virology , Potexvirus*/genetics , Potexvirus*/isolation & purification , Potexvirus*/classification , Plant Diseases*/virology , Genome, Viral*, RNA, Viral/genetics ; Brazil ; Phylogeny ; Genetic Variation ; High-Throughput Nucleotide Sequencing
Περίληψη: Objective: Yam virus X (YVX; Potexvirus ecsdioscoreae) is a positive-sense, flexuous RNA virus belonging to the family Alphaflexiviridae. It has been first reported from Guadeloupe, a French archipelago located in the Caribbean Sea. In this study, we investigated the virome in yam (Dioscorea spp.) plant material collected in the state of Bahia (Brazil) by high-throughput sequencing (HTS) on Illumina platform. The objective of the investigation was to explore the occurrence of YVX in yam from South America, and to study its genetic diversity compared to the only one YVX genome sequence available in the GenBank public database.
Results: An initial investigation by HTS of bulked RNA extracts (n=23, combined into 4 pools) revealed occurrence of YVX only in samples collected in the region of Valença. Subsequent screening by RT-PCR of the individual samples composing the pool uncovered infection with YVX only in Discorea trifida. Total RNA extracts from three infected plants were individually sequenced, resulting in the assembly of three complete genome sequences of YVX, showing ~84% nucleotide identity to the reference sequence from Guadeloupe. Our results contribute to expanding the pool of sequences available for YVX, supporting detection purposes and stimulating additional investigations for future studies on YVX diversity and evolution.
(© 2026. The Author(s).)
Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.
References: Virus Genes. 2022 Aug;58(4):294-307. (PMID: 35538384)
Mol Biol Evol. 2024 Dec 6;41(12):. (PMID: 39708372)
Plants (Basel). 2019 Jun 11;8(6):. (PMID: 31212654)
Viruses. 2022 Mar 23;14(4):. (PMID: 35458392)
Viruses. 2022 Aug 26;14(9):. (PMID: 36146691)
Arch Virol. 2017 Jan;162(1):317-319. (PMID: 27730382)
Crit Rev Biochem Mol Biol. 1993;28(5):375-430. (PMID: 8269709)
Nucleic Acids Res. 2024 Jul 5;52(W1):W521-W525. (PMID: 38597606)
J Gen Virol. 1988 Aug;69 ( Pt 8):1789-98. (PMID: 3404114)
Viruses. 2020 Sep 29;12(10):. (PMID: 33003342)
Arch Virol. 2013 Feb;158(2):515-8. (PMID: 23081678)
J Gen Virol. 2020 Jul;101(7):699-700. (PMID: 32525472)
J Ethnobiol Ethnomed. 2024 Feb 2;20(1):13. (PMID: 38308263)
Braz J Biol. 2015 Jan-Mar;75(1):104-13. (PMID: 25945627)
Arch Virol. 2014 Dec;159(12):3421-6. (PMID: 25204410)
Viruses. 2016 Jul 07;8(7):. (PMID: 27399761)
Contributed Indexing: Keywords: Bioinformatics; Illumina sequencing; Plant virus; Potexvirus; South America
Substance Nomenclature: 0 (RNA, Viral)
Entry Date(s): Date Created: 20260903 Date Completed: 20260903 Latest Revision: 20260905
Update Code: 20260905
PubMed Central ID: PMC13540820
DOI: 10.1186/s13104-026-07987-0
PMID: 42687209
Βάση Δεδομένων: MEDLINE
FullText Text:
  Availability: 0
CustomLinks:
  – Url: https://resolver.ebsco.com/c/fiv2js/result?sid=EBSCO:cmedm&genre=article&issn=17560500&ISBN=&volume=19&issue=1&date=20260902&spage=&pages=&title=BMC research notes&atitle=Characterization%20of%20yam%20virus%20X%20isolates%20from%20Dioscorea%20trifida%20in%20Brazil.&aulast=Ara%C3%BAjo%20CPFS&id=DOI:10.1186/s13104-026-07987-0
    Name: Full Text Finder (for New FTF UI) (ns324271)
    Category: fullText
    Text: Full Text Finder
    MouseOverText: Full Text Finder
Header DbId: cmedm
DbLabel: MEDLINE
An: 42687209
AccessLevel: 3
PubType: Academic Journal
PubTypeId: academicJournal
PreciseRelevancyScore: 0
IllustrationInfo
Items – Name: Title
  Label: Title
  Group: Ti
  Data: Characterization of yam virus X isolates from Dioscorea trifida in Brazil.
– Name: Author
  Label: Authors
  Group: Au
  Data: <searchLink fieldCode="AU" term="%22Araújo+CPFS%22">Araújo CPFS</searchLink>; Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7B, 38124, Brunswick, Germany.<br /><searchLink fieldCode="AU" term="%22Knierim+D%22">Knierim D</searchLink>; Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7B, 38124, Brunswick, Germany.<br /><searchLink fieldCode="AU" term="%22de+Oliveira+SAS%22">de Oliveira SAS</searchLink>; Embrapa Mandioca e Fruticultura, Rua Embrapa S/nº, Chapadinha, Bahia, 44380-000, Cruz das Almas, Brazil.<br /><searchLink fieldCode="AU" term="%22Blawid+R%22">Blawid R</searchLink>; Department of Agronomy, Federal Rural University of Pernambuco, Rua Dom Manuel de Medeiros S/nº, Dois Irmãos, Pernambuco, 52171-900, Recife, Brazil.<br /><searchLink fieldCode="AU" term="%22Margaria+P%22">Margaria P</searchLink>; Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7B, 38124, Brunswick, Germany. paolo.margaria@dsmz.de.
– Name: TitleSource
  Label: Source
  Group: Src
  Data: <searchLink fieldCode="JN" term="%22101462768%22">BMC research notes</searchLink> [BMC Res Notes] 2026 Sep 02; Vol. 19 (1). <i>Date of Electronic Publication: </i>2026 Sep 02.
– Name: TypePub
  Label: Publication Type
  Group: TypPub
  Data: Journal Article
– Name: Language
  Label: Language
  Group: Lang
  Data: English
– Name: TitleSource
  Label: Journal Info
  Group: Src
  Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Biomed+Central%22">Biomed Central </searchLink><i>Country of Publication: </i>England <i>NLM ID: </i>101462768 <i>Publication Model: </i>Electronic <i>Cited Medium: </i>Internet <i>ISSN: </i>1756-0500 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2217560500%22">17560500 </searchLink><i>NLM ISO Abbreviation: </i>BMC Res Notes <i>Subsets: </i>MEDLINE
– Name: PublisherInfo
  Label: Imprint Name(s)
  Group: PubInfo
  Data: <i>Original Publication</i>: London : Biomed Central, 2008.
– Name: SubjectMESH
  Label: MeSH Terms
  Group: Su
  Data: <searchLink fieldCode="MM" term="%22Dioscorea%22">Dioscorea*</searchLink>/<searchLink fieldCode="MM" term="%22Dioscorea+virology%22">virology</searchLink> <br /><searchLink fieldCode="MM" term="%22Potexvirus%22">Potexvirus*</searchLink>/<searchLink fieldCode="MM" term="%22Potexvirus+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Potexvirus%22">Potexvirus*</searchLink>/<searchLink fieldCode="MM" term="%22Potexvirus+isolation+%26+purification%22">isolation & purification</searchLink> <br /><searchLink fieldCode="MM" term="%22Potexvirus%22">Potexvirus*</searchLink>/<searchLink fieldCode="MM" term="%22Potexvirus+classification%22">classification</searchLink> <br /><searchLink fieldCode="MM" term="%22Plant+Diseases%22">Plant Diseases*</searchLink>/<searchLink fieldCode="MM" term="%22Plant+Diseases+virology%22">virology</searchLink> <br /><searchLink fieldCode="MM" term="%22Genome%2C+Viral%22">Genome, Viral*</searchLink><br /><searchLink fieldCode="MH" term="%22RNA%2C+Viral%22">RNA, Viral</searchLink>/<searchLink fieldCode="MH" term="%22RNA%2C+Viral+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Brazil%22">Brazil</searchLink> ; <searchLink fieldCode="MH" term="%22Phylogeny%22">Phylogeny</searchLink> ; <searchLink fieldCode="MH" term="%22Genetic+Variation%22">Genetic Variation</searchLink> ; <searchLink fieldCode="MH" term="%22High-Throughput+Nucleotide+Sequencing%22">High-Throughput Nucleotide Sequencing</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: Objective: Yam virus X (YVX; Potexvirus ecsdioscoreae) is a positive-sense, flexuous RNA virus belonging to the family Alphaflexiviridae. It has been first reported from Guadeloupe, a French archipelago located in the Caribbean Sea. In this study, we investigated the virome in yam (Dioscorea spp.) plant material collected in the state of Bahia (Brazil) by high-throughput sequencing (HTS) on Illumina platform. The objective of the investigation was to explore the occurrence of YVX in yam from South America, and to study its genetic diversity compared to the only one YVX genome sequence available in the GenBank public database.<br />Results: An initial investigation by HTS of bulked RNA extracts (n=23, combined into 4 pools) revealed occurrence of YVX only in samples collected in the region of Valença. Subsequent screening by RT-PCR of the individual samples composing the pool uncovered infection with YVX only in Discorea trifida. Total RNA extracts from three infected plants were individually sequenced, resulting in the assembly of three complete genome sequences of YVX, showing ~84% nucleotide identity to the reference sequence from Guadeloupe. Our results contribute to expanding the pool of sequences available for YVX, supporting detection purposes and stimulating additional investigations for future studies on YVX diversity and evolution.<br /> (© 2026. The Author(s).)
– Name: Abstract
  Label: Competing Interests
  Group: Ab
  Data: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.
– Name: Ref
  Label: References
  Group: RefInfo
  Data: Virus Genes. 2022 Aug;58(4):294-307. (PMID: <searchLink fieldCode="PM" term="%2235538384%22">35538384)</searchLink><br />Mol Biol Evol. 2024 Dec 6;41(12):. (PMID: <searchLink fieldCode="PM" term="%2239708372%22">39708372)</searchLink><br />Plants (Basel). 2019 Jun 11;8(6):. (PMID: <searchLink fieldCode="PM" term="%2231212654%22">31212654)</searchLink><br />Viruses. 2022 Mar 23;14(4):. (PMID: <searchLink fieldCode="PM" term="%2235458392%22">35458392)</searchLink><br />Viruses. 2022 Aug 26;14(9):. (PMID: <searchLink fieldCode="PM" term="%2236146691%22">36146691)</searchLink><br />Arch Virol. 2017 Jan;162(1):317-319. (PMID: <searchLink fieldCode="PM" term="%2227730382%22">27730382)</searchLink><br />Crit Rev Biochem Mol Biol. 1993;28(5):375-430. (PMID: <searchLink fieldCode="PM" term="%228269709%22">8269709)</searchLink><br />Nucleic Acids Res. 2024 Jul 5;52(W1):W521-W525. (PMID: <searchLink fieldCode="PM" term="%2238597606%22">38597606)</searchLink><br />J Gen Virol. 1988 Aug;69 ( Pt 8):1789-98. (PMID: <searchLink fieldCode="PM" term="%223404114%22">3404114)</searchLink><br />Viruses. 2020 Sep 29;12(10):. (PMID: <searchLink fieldCode="PM" term="%2233003342%22">33003342)</searchLink><br />Arch Virol. 2013 Feb;158(2):515-8. (PMID: <searchLink fieldCode="PM" term="%2223081678%22">23081678)</searchLink><br />J Gen Virol. 2020 Jul;101(7):699-700. (PMID: <searchLink fieldCode="PM" term="%2232525472%22">32525472)</searchLink><br />J Ethnobiol Ethnomed. 2024 Feb 2;20(1):13. (PMID: <searchLink fieldCode="PM" term="%2238308263%22">38308263)</searchLink><br />Braz J Biol. 2015 Jan-Mar;75(1):104-13. (PMID: <searchLink fieldCode="PM" term="%2225945627%22">25945627)</searchLink><br />Arch Virol. 2014 Dec;159(12):3421-6. (PMID: <searchLink fieldCode="PM" term="%2225204410%22">25204410)</searchLink><br />Viruses. 2016 Jul 07;8(7):. (PMID: <searchLink fieldCode="PM" term="%2227399761%22">27399761)</searchLink>
– Name: SubjectMinor
  Label: Contributed Indexing
  Group:
  Data: <i>Keywords: </i>Bioinformatics; Illumina sequencing; Plant virus; Potexvirus; South America
– Name: NumberCAS
  Label: Substance Nomenclature
  Group: ID
  Data: 0 (RNA, Viral)
– Name: DateEntry
  Label: Entry Date(s)
  Group: Date
  Data: <i>Date Created: </i>20260903 <i>Date Completed: </i>20260903 <i>Latest Revision: </i>20260905
– Name: DateUpdate
  Label: Update Code
  Group: Date
  Data: 20260905
– Name: PubmedCentralID
  Label: PubMed Central ID
  Group: ID
  Data: PMC13540820
– Name: DOI
  Label: DOI
  Group: ID
  Data: 10.1186/s13104-026-07987-0
– Name: AN
  Label: PMID
  Group: ID
  Data: 42687209
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=cmedm&AN=42687209
RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.1186/s13104-026-07987-0
    Languages:
      – Code: eng
        Text: English
    Subjects:
      – SubjectFull: RNA, Viral genetics
        Type: general
      – SubjectFull: Brazil
        Type: general
      – SubjectFull: Phylogeny
        Type: general
      – SubjectFull: Genetic Variation
        Type: general
      – SubjectFull: High-Throughput Nucleotide Sequencing
        Type: general
      – SubjectFull: Dioscorea virology
        Type: general
      – SubjectFull: Potexvirus genetics
        Type: general
      – SubjectFull: Potexvirus isolation & purification
        Type: general
      – SubjectFull: Potexvirus classification
        Type: general
      – SubjectFull: Plant Diseases virology
        Type: general
      – SubjectFull: Genome, Viral
        Type: general
    Titles:
      – TitleFull: Characterization of yam virus X isolates from Dioscorea trifida in Brazil.
        Type: main
  BibRelationships:
    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Araújo CPFS
      – PersonEntity:
          Name:
            NameFull: Knierim D
      – PersonEntity:
          Name:
            NameFull: de Oliveira SAS
      – PersonEntity:
          Name:
            NameFull: Blawid R
      – PersonEntity:
          Name:
            NameFull: Margaria P
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 02
              M: 09
              Text: 2026 Sep 02
              Type: published
              Y: 2026
          Identifiers:
            – Type: issn-electronic
              Value: 1756-0500
          Numbering:
            – Type: volume
              Value: 19
            – Type: issue
              Value: 1
          Titles:
            – TitleFull: BMC research notes
              Type: main
ResultId 1