A Survey Using High-Throughput Sequencing Suggests That the Diversity of Cereal and Barley Yellow Dwarf Viruses Is Underestimated
Worldwide, barley/cereal yellow dwarf viruses (YDVs) are the most widespread and damaging group of cereal viruses. In this study, we applied high-throughput sequencing technologies (HTS) to perform a virus survey on symptomatic plants from 47 cereal fields in Estonia. HTS allowed the assembly of com...
Saved in:
| Published in: | Frontiers in microbiology Vol. 12; p. 673218 |
|---|---|
| Main Authors: | , , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
Frontiers Media
11.05.2021
Frontiers Media S.A |
| Subjects: | |
| ISSN: | 1664-302X, 1664-302X |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Abstract | Worldwide, barley/cereal yellow dwarf viruses (YDVs) are the most widespread and damaging group of cereal viruses. In this study, we applied high-throughput sequencing technologies (HTS) to perform a virus survey on symptomatic plants from 47 cereal fields in Estonia. HTS allowed the assembly of complete genome sequences for 22 isolates of cereal yellow dwarf virus RPS, barley yellow dwarf virus GAV, barley yellow dwarf virus PAS (BYDV-PAS), barley yellow dwarf virus PAV (BYDV-PAV), and barley yellow dwarf virus OYV (BYDV-OYV). We also assembled a near-complete genome of the putative novel species BYDV-OYV from Swedish samples of meadow fescue. Previously, partial sequencing of the central part of the coat protein gene indicated that BYDV-OYV represented a putative new species closely related to BYDV-PAV-CN, which currently is recognized as a subtype of BYDV-PAV. The present study found that whereas the 3′gene block of BYDV-OYV shares the closest relationship with BYDV-PAV-CN, the 5′gene block of BYDV-OYV shows the closest relationships to that of BYDV-PAS. Recombination detection analysis revealed that BYDV-OYV is a parental virus for both. Analysis of complete genome sequence data indicates that both BYDV-OYV and BYDV-PAV-CN meet the species criteria of genus
Luteovirus
. The study discusses BYDV phylogeny, and through a systematic
in silico
analysis of published primers for YDV detection, the existing gaps in current diagnostic practices for detection of YDVs, proposing primer pairs based on the most recent genomic information for the detection of different BYDV species. Thanks to the rising number of sequences available in databases, continuous updating of diagnostic primers can improve test specificity, e.g., inclusivity and exclusivity at species levels. This is needed to properly survey the geographical and host distribution of the different species of the YDV complex and their prevalence in cereal/barley yellow dwarf disease epidemics. |
|---|---|
| AbstractList | Worldwide, barley/cereal yellow dwarf viruses (YDVs) are the most widespread and damaging group of cereal viruses. In this study, we applied high-throughput sequencing technologies (HTS) to perform a virus survey on symptomatic plants from 47 cereal fields in Estonia. HTS allowed the assembly of complete genome sequences for 22 isolates of cereal yellow dwarf virus RPS, barley yellow dwarf virus GAV, barley yellow dwarf virus PAS (BYDV-PAS), barley yellow dwarf virus PAV (BYDV-PAV), and barley yellow dwarf virus OYV (BYDV-OYV). We also assembled a near-complete genome of the putative novel species BYDV-OYV from Swedish samples of meadow fescue. Previously, partial sequencing of the central part of the coat protein gene indicated that BYDV-OYV represented a putative new species closely related to BYDV-PAV-CN, which currently is recognized as a subtype of BYDV-PAV. The present study found that whereas the 3′gene block of BYDV-OYV shares the closest relationship with BYDV-PAV-CN, the 5′gene block of BYDV-OYV shows the closest relationships to that of BYDV-PAS. Recombination detection analysis revealed that BYDV-OYV is a parental virus for both. Analysis of complete genome sequence data indicates that both BYDV-OYV and BYDV-PAV-CN meet the species criteria of genus Luteovirus. The study discusses BYDV phylogeny, and through a systematic in silico analysis of published primers for YDV detection, the existing gaps in current diagnostic practices for detection of YDVs, proposing primer pairs based on the most recent genomic information for the detection of different BYDV species. Thanks to the rising number of sequences available in databases, continuous updating of diagnostic primers can improve test specificity, e.g., inclusivity and exclusivity at species levels. This is needed to properly survey the geographical and host distribution of the different species of the YDV complex and their prevalence in cereal/barley yellow dwarf disease epidemics. Worldwide, barley/cereal yellow dwarf viruses (YDVs) are the most widespread and damaging group of cereal viruses. In this study, we applied high-throughput sequencing technologies (HTS) to perform a virus survey on symptomatic plants from 47 cereal fields in Estonia. HTS allowed the assembly of complete genome sequences for 22 isolates of cereal yellow dwarf virus RPS, barley yellow dwarf virus GAV, barley yellow dwarf virus PAS (BYDV-PAS), barley yellow dwarf virus PAV (BYDV-PAV), and barley yellow dwarf virus OYV (BYDV-OYV). We also assembled a near-complete genome of the putative novel species BYDV-OYV from Swedish samples of meadow fescue. Previously, partial sequencing of the central part of the coat protein gene indicated that BYDV-OYV represented a putative new species closely related to BYDV-PAV-CN, which currently is recognized as a subtype of BYDV-PAV. The present study found that whereas the 3′gene block of BYDV-OYV shares the closest relationship with BYDV-PAV-CN, the 5′gene block of BYDV-OYV shows the closest relationships to that of BYDV-PAS. Recombination detection analysis revealed that BYDV-OYV is a parental virus for both. Analysis of complete genome sequence data indicates that both BYDV-OYV and BYDV-PAV-CN meet the species criteria of genus Luteovirus . The study discusses BYDV phylogeny, and through a systematic in silico analysis of published primers for YDV detection, the existing gaps in current diagnostic practices for detection of YDVs, proposing primer pairs based on the most recent genomic information for the detection of different BYDV species. Thanks to the rising number of sequences available in databases, continuous updating of diagnostic primers can improve test specificity, e.g., inclusivity and exclusivity at species levels. This is needed to properly survey the geographical and host distribution of the different species of the YDV complex and their prevalence in cereal/barley yellow dwarf disease epidemics. Worldwide, barley/cereal yellow dwarf viruses (YDVs) are the most widespread and damaging group of cereal viruses. In this study, we applied high-throughput sequencing technologies (HTS) to perform a virus survey on symptomatic plants from 47 cereal fields in Estonia. HTS allowed the assembly of complete genome sequences for 22 isolates of cereal yellow dwarf virus RPS, barley yellow dwarf virus GAV, barley yellow dwarf virus PAS (BYDV-PAS), barley yellow dwarf virus PAV (BYDV-PAV), and barley yellow dwarf virus OYV (BYDV-OYV). We also assembled a near-complete genome of the putative novel species BYDV-OYV from Swedish samples of meadow fescue. Previously, partial sequencing of the central part of the coat protein gene indicated that BYDV-OYV represented a putative new species closely related to BYDV-PAV-CN, which currently is recognized as a subtype of BYDV-PAV. The present study found that whereas the 3'gene block of BYDV-OYV shares the closest relationship with BYDV-PAV-CN, the 5'gene block of BYDV-OYV shows the closest relationships to that of BYDV-PAS. Recombination detection analysis revealed that BYDV-OYV is a parental virus for both. Analysis of complete genome sequence data indicates that both BYDV-OYV and BYDV-PAV-CN meet the species criteria of genus Luteovirus. The study discusses BYDV phylogeny, and through a systematic in silico analysis of published primers for YDV detection, the existing gaps in current diagnostic practices for detection of YDVs, proposing primer pairs based on the most recent genomic information for the detection of different BYDV species. Thanks to the rising number of sequences available in databases, continuous updating of diagnostic primers can improve test specificity, e.g., inclusivity and exclusivity at species levels. This is needed to properly survey the geographical and host distribution of the different species of the YDV complex and their prevalence in cereal/barley yellow dwarf disease epidemics.Worldwide, barley/cereal yellow dwarf viruses (YDVs) are the most widespread and damaging group of cereal viruses. In this study, we applied high-throughput sequencing technologies (HTS) to perform a virus survey on symptomatic plants from 47 cereal fields in Estonia. HTS allowed the assembly of complete genome sequences for 22 isolates of cereal yellow dwarf virus RPS, barley yellow dwarf virus GAV, barley yellow dwarf virus PAS (BYDV-PAS), barley yellow dwarf virus PAV (BYDV-PAV), and barley yellow dwarf virus OYV (BYDV-OYV). We also assembled a near-complete genome of the putative novel species BYDV-OYV from Swedish samples of meadow fescue. Previously, partial sequencing of the central part of the coat protein gene indicated that BYDV-OYV represented a putative new species closely related to BYDV-PAV-CN, which currently is recognized as a subtype of BYDV-PAV. The present study found that whereas the 3'gene block of BYDV-OYV shares the closest relationship with BYDV-PAV-CN, the 5'gene block of BYDV-OYV shows the closest relationships to that of BYDV-PAS. Recombination detection analysis revealed that BYDV-OYV is a parental virus for both. Analysis of complete genome sequence data indicates that both BYDV-OYV and BYDV-PAV-CN meet the species criteria of genus Luteovirus. The study discusses BYDV phylogeny, and through a systematic in silico analysis of published primers for YDV detection, the existing gaps in current diagnostic practices for detection of YDVs, proposing primer pairs based on the most recent genomic information for the detection of different BYDV species. Thanks to the rising number of sequences available in databases, continuous updating of diagnostic primers can improve test specificity, e.g., inclusivity and exclusivity at species levels. This is needed to properly survey the geographical and host distribution of the different species of the YDV complex and their prevalence in cereal/barley yellow dwarf disease epidemics. |
| Author | Massart, Sébastien Sooväli, Pille Kvarnheden, Anders Sõmera, Merike Tamisier, Lucie Sathees, Kanitha |
| AuthorAffiliation | 3 Department of Plant Protection, Estonian Crop Research Institute , Jõgeva , Estonia 2 Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech – University of Liège , Gembloux , Belgium 5 Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences , Tartu , Estonia 4 Department of Plant Biology, Swedish University of Agricultural Sciences , Uppsala , Sweden 1 Department of Chemistry and Biotechnology, Tallinn University of Technology , Tallinn , Estonia |
| AuthorAffiliation_xml | – name: 5 Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences , Tartu , Estonia – name: 4 Department of Plant Biology, Swedish University of Agricultural Sciences , Uppsala , Sweden – name: 1 Department of Chemistry and Biotechnology, Tallinn University of Technology , Tallinn , Estonia – name: 2 Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech – University of Liège , Gembloux , Belgium – name: 3 Department of Plant Protection, Estonian Crop Research Institute , Jõgeva , Estonia |
| Author_xml | – sequence: 1 givenname: Merike surname: Sõmera fullname: Sõmera, Merike – sequence: 2 givenname: Sébastien surname: Massart fullname: Massart, Sébastien – sequence: 3 givenname: Lucie surname: Tamisier fullname: Tamisier, Lucie – sequence: 4 givenname: Pille surname: Sooväli fullname: Sooväli, Pille – sequence: 5 givenname: Kanitha surname: Sathees fullname: Sathees, Kanitha – sequence: 6 givenname: Anders surname: Kvarnheden fullname: Kvarnheden, Anders |
| BackLink | https://hal.inrae.fr/hal-04107128$$DView record in HAL https://res.slu.se/id/publ/112238$$DView record from Swedish Publication Index (Sveriges lantbruksuniversitet) |
| BookMark | eNp1Uk1v1DAQjVARLaU_gJuPcNjFX9k4F6SyBbrSShx2F8HJsp1x4iqbFNvZao_8c5xNkWgl5uAZzcx786yZ19lZ13eQZW8JnjMmyg9274yeU0zJfFEwSsSL7IIsFnzGMP1x9k98nl2FcIeTcUzT-yo7ZxzzBab5Rfb7Gm0Gf4Aj2gXX1ejW1c1s2_h-qJv7IaIN_BqgM2NpM9Q1hBjQtlERxQbQjTuADy4eUW_REjyoFqmuQp-UbxPjT2jb_gHdPChv0XfnhwABrQLadVXqDdHtVYTqTfbSqjbA1aO_zHZfPm-Xt7P1t6-r5fV6ZvK8jDPChNV5RanKc2pEkRPIGa5KUWqsLKYVS1YYzStrFeTKCGW5EmVRQk6xZewyW028Va_u5L1P0_1R9srJU6L3tVQ-OtOC1JyXmFRKK9BcY6OtxsJYIXJWYWN14ppPXOEB7gf9hC20g1Z-dDKAJIRSJhLg4wRI3XuoDHTRq_YJ7mmlc42s-4MUhHNe8ETAJoLWQQ1JrXbyQE_AUzy0Sb6RGiSlCyFpSYgY__x-QjXPht1er-WYw5zgglBxIKn33aNE36edhyj3Lpi0QtVBPwRJc8YXhFMyiimmVuP7EDxYaVxU0fWjdtdKguV4ovJ0onI8UTmdaEKSZ8i_qv6P-QN9Gu2U |
| CitedBy_id | crossref_primary_10_1071_CP24283 crossref_primary_10_15212_ijafr_2022_0108 crossref_primary_10_1146_annurev_phyto_121421_125135 crossref_primary_10_1111_pce_15204 crossref_primary_10_15212_ijafr_2023_0110 crossref_primary_10_1094_PHYTO_10_23_0394_KC crossref_primary_10_1007_s00705_023_05890_8 crossref_primary_10_3390_v13122530 crossref_primary_10_3390_ijms232315074 crossref_primary_10_1111_ppa_70013 crossref_primary_10_1111_ppa_13871 crossref_primary_10_15212_ijafr_2023_0115 |
| Cites_doi | 10.1007/s10658-005-1231-y 10.1007/s00705-012-1294-y 10.1007/s00705-006-0913-x 10.1099/vir.0.81834-0 10.1016/S2095-3119(19)62805-4 10.1111/j.1365-3059.2012.02644.x 10.1371/journal.ppat.1004868 10.1556/crc.37.2009.4.7 10.3390/v10070385 10.1007/s13313-012-0133-7 10.1016/j.biochi.2010.09.017 10.1093/molbev/msp259 10.1093/bioinformatics/bts094 10.1094/phyto-86-370 10.1016/j.jviromet.2010.06.003 10.1128/jvi.02160-09 10.1094/PDIS-11-18-2059-PDN 10.3389/fmicb.2018.00939 10.1007/s00705-015-2686-6 10.3390/v8050120 10.1016/s0966-842x(98)01384-5 10.1146/annurev.py.28.090190.002013 10.1046/j.1364-3703.2002.00112.x 10.1371/journal.pone.0016896 10.1099/0022-1317-72-6-1473 10.1080/713608119 10.1016/j.jviromet.2010.06.020 10.1007/978-94-007-0791-7_13 10.1007/s00705-003-0242-2 10.1016/j.jviromet.2004.04.005 10.1094/pd-66-381 10.1016/j.jviromet.2007.10.015 10.1094/PHYTO-07-19-0258-FI 10.1007/s00705-007-0947-8 10.1128/jvi.73.4.2876-2885.1999 10.1007/s00705-016-2881-0 10.1002/ps.5851 10.1007/s00705-009-0415-8 10.1094/PDIS-04-16-0426-PDN 10.1094/phyto.2003.93.11.1386 10.1016/j.virusres.2017.07.006 10.1371/journal.pone.0067231 10.1094/php-09-17-0056-rs 10.3389/fmicb.2017.01689 |
| ContentType | Journal Article |
| Copyright | Copyright © 2021 Sõmera, Massart, Tamisier, Sooväli, Sathees and Kvarnheden. licence_http://creativecommons.org/publicdomain/zero Copyright © 2021 Sõmera, Massart, Tamisier, Sooväli, Sathees and Kvarnheden. 2021 Sõmera, Massart, Tamisier, Sooväli, Sathees and Kvarnheden |
| Copyright_xml | – notice: Copyright © 2021 Sõmera, Massart, Tamisier, Sooväli, Sathees and Kvarnheden. – notice: licence_http://creativecommons.org/publicdomain/zero – notice: Copyright © 2021 Sõmera, Massart, Tamisier, Sooväli, Sathees and Kvarnheden. 2021 Sõmera, Massart, Tamisier, Sooväli, Sathees and Kvarnheden |
| CorporateAuthor | Sveriges lantbruksuniversitet |
| CorporateAuthor_xml | – name: Sveriges lantbruksuniversitet |
| DBID | AAYXX CITATION 7X8 1XC VOOES JLOSS Q33 5PM ADTPV AOWAS DOA |
| DOI | 10.3389/fmicb.2021.673218 |
| DatabaseName | CrossRef MEDLINE - Academic Hyper Article en Ligne (HAL) Hyper Article en Ligne (HAL) (Open Access) Université de Liège - Open Repository and Bibliography (ORBI) (Open Access titles only) Université de Liège - Open Repository and Bibliography (ORBI) PubMed Central (Full Participant titles) SwePub SwePub Articles DOAJ Directory of Open Access Journals |
| DatabaseTitle | CrossRef MEDLINE - Academic |
| DatabaseTitleList | CrossRef MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: DOA name: DOAJ Open Access Full Text url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1664-302X |
| ExternalDocumentID | oai_doaj_org_article_b44901dabaeb4b0cbfb08cf8853d0cfb oai_slubar_slu_se_112238 PMC8144474 oai_orbi_ulg_ac_be_2268_291183 oai:HAL:hal-04107128v1 10_3389_fmicb_2021_673218 |
| GroupedDBID | 53G 5VS 9T4 AAFWJ AAKDD AAYXX ACGFO ACGFS ADBBV ADRAZ AENEX AFPKN ALMA_UNASSIGNED_HOLDINGS AOIJS BAWUL BCNDV CITATION DIK ECGQY GROUPED_DOAJ GX1 HYE KQ8 M48 M~E O5R O5S OK1 PGMZT RNS RPM 7X8 1XC VOOES JLOSS Q33 5PM ADTPV AOWAS IPNFZ RIG |
| ID | FETCH-LOGICAL-c559t-138fb5d22a552c8751e530d989b0af02d33337cb4dffae5ac8af4a8979e520f33 |
| IEDL.DBID | DOA |
| ISICitedReferencesCount | 16 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000653629300001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 1664-302X |
| IngestDate | Fri Oct 03 12:35:45 EDT 2025 Tue Nov 04 16:49:30 EST 2025 Tue Sep 30 15:57:27 EDT 2025 Sat Nov 29 01:28:37 EST 2025 Thu Nov 27 06:49:35 EST 2025 Fri Sep 05 06:43:01 EDT 2025 Sat Nov 29 02:30:16 EST 2025 Tue Nov 18 21:38:42 EST 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Language | English |
| License | licence_http://creativecommons.org/publicdomain/zero/: http://creativecommons.org/publicdomain/zero This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c559t-138fb5d22a552c8751e530d989b0af02d33337cb4dffae5ac8af4a8979e520f33 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 scopus-id:2-s2.0-85107234400 Edited by: Xifeng Wang, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection (CAAS), China Reviewed by: W. Allen Miller, Iowa State University, United States; Peipei Zhang, Langfang Normal University, China This article was submitted to Microbe and Virus Interactions with Plants, a section of the journal Frontiers in Microbiology |
| ORCID | 0000-0002-9231-2997 0000-0002-7153-737X |
| OpenAccessLink | https://doaj.org/article/b44901dabaeb4b0cbfb08cf8853d0cfb |
| PMID | 34046025 |
| PQID | 2534614214 |
| PQPubID | 23479 |
| ParticipantIDs | doaj_primary_oai_doaj_org_article_b44901dabaeb4b0cbfb08cf8853d0cfb swepub_primary_oai_slubar_slu_se_112238 pubmedcentral_primary_oai_pubmedcentral_nih_gov_8144474 liege_orbi_v2_oai_orbi_ulg_ac_be_2268_291183 hal_primary_oai_HAL_hal_04107128v1 proquest_miscellaneous_2534614214 crossref_citationtrail_10_3389_fmicb_2021_673218 crossref_primary_10_3389_fmicb_2021_673218 |
| PublicationCentury | 2000 |
| PublicationDate | 2021-05-11 |
| PublicationDateYYYYMMDD | 2021-05-11 |
| PublicationDate_xml | – month: 05 year: 2021 text: 2021-05-11 day: 11 |
| PublicationDecade | 2020 |
| PublicationTitle | Frontiers in microbiology |
| PublicationYear | 2021 |
| Publisher | Frontiers Media Frontiers Media S.A |
| Publisher_xml | – name: Frontiers Media – name: Frontiers Media S.A |
| References | Martin (B22) 2015; 1 Zhang (B50) 2009; 154 Nagy (B27) 2006; 10 Kamali (B14) 2016; 161 Martin (B23) 1990; 28 Pallett (B30) 2010; 168 Svanella-Dumas (B44) 2013; 8 Katsiani (B15) 2018; 10 Zhao (B52) 2010; 169 Pagan (B29) 2010; 84 Miller (B25) 1995; 14 Rastgou (B32) 2005; 113 Rochow (B35) 1982; 1982 Balaji (B1) 2003; 93 Miller (B26) 2002; 3 Boulila (B3) 2011; 93 Robertson (B33) 2007; 152 Parry (B31) 2012; 41 Jarošová (B13) 2013; 62 Henry (B12) 2003 Halbert (B10) 1995 Zhang (B49) 2017; 8 Liu (B19) 2007; 152 Zhao (B51) 2016; 161 Hall (B11) 2006; 87 Koev (B16) 1999; 73 Robertson (B34) 1991; 72 Sõmera (B42) 2020; 110 Malmstrom (B20) 2017; 241 D’Arcy (B6) 1995 Zhou (B53) 1990 Kundu (B17) 2009; 37 Signoret (B38) 1990 Sõmera (B43) 2019; 103 Van den Eynde (B47) 2020; 76 Gouy (B9) 2010; 27 Laney (B18) 2018; 19 Gildow (B8) 1990 Bisnieks (B2) 2004; 149 Tao (B45) 2012; 157 Najar (B28) 2017; 56 Wu (B48) 2011; 6 Santala (B36) 2018; 9 Deb (B7) 2008; 148 Miller (B24) 1998; 6 Sõmera (B41) 2016; 100 Smirnova (B40) 2015; 11 Malmstrom (B21) 2004; 120 Trzmeil (B46) 2017; 99 Chay (B4) 1996; 86 Schulz (B37) 2012; 8 Chen (B5) 2016; 8 Singh (B39) 2020; 19 |
| References_xml | – volume: 113 start-page: 321 year: 2005 ident: B32 article-title: Relationships of Barley yellow dwarf virus-PAV and Cereal yellow dwarf virus-RPV from Iran with viruses of the family Luteoviridae. publication-title: Eur. J. Plant Pathol. doi: 10.1007/s10658-005-1231-y – volume: 157 start-page: 1261 year: 2012 ident: B45 article-title: Development of a multiplex polymerase chain reaction for simultaneous detection of wheat viruses and a phytoplasma in China. publication-title: Arch. Virol. doi: 10.1007/s00705-012-1294-y – volume: 1 year: 2015 ident: B22 article-title: RDP4: Detection and analysis of recombination patterns in virus genomes. publication-title: Virus Evolut. – start-page: 42 year: 1990 ident: B38 article-title: The barley yellow dwarf virus situation in Western Europe publication-title: World perspectives on Barley yellow dwarf – volume: 99 start-page: 493 year: 2017 ident: B46 article-title: Identification of barley yellow dwarf viruses in Poland. publication-title: J. Plant Pathol. – volume: 152 start-page: 891 year: 2007 ident: B33 article-title: Genetic structure in natural populations of barley/cereal yellow dwarf virus isolates from Alaska. publication-title: Arch. Virol. doi: 10.1007/s00705-006-0913-x – volume: 87 start-page: 3067 year: 2006 ident: B11 article-title: Selective constraint and genetic differentiation in geographically distant barley yellow dwarf virus populations. publication-title: J. Gen. Virol. doi: 10.1099/vir.0.81834-0 – volume: 19 start-page: 1825 year: 2020 ident: B39 article-title: Virome identification in wheat in the Czech Republic using small RNA deep sequencing. publication-title: J. Integr. Agric. doi: 10.1016/S2095-3119(19)62805-4 – volume: 62 start-page: 436 year: 2013 ident: B13 article-title: A comparative study of the barley yellow dwarf virus species PAV and PAS: distribution, virus accumulation and host resistance. publication-title: Plant Pathol. doi: 10.1111/j.1365-3059.2012.02644.x – volume: 11 year: 2015 ident: B40 article-title: Discovery of a small non-AUG-initiated ORF in poleroviruses and luteoviruses that is required for long-distance movement. publication-title: PLoS Pathog. doi: 10.1371/journal.ppat.1004868 – volume: 37 start-page: 541 year: 2009 ident: B17 article-title: Discrimination of three BYDV species by one-step RT-PCR-RFLP and sequence based methods in cereal plants from the Czech Republic. publication-title: Cereal Res. Commun. doi: 10.1556/crc.37.2009.4.7 – volume: 10 year: 2018 ident: B15 article-title: High-throughput sequencing reveals further diversity of little cherry virus 1 with implications for diagnostics. publication-title: Viruses doi: 10.3390/v10070385 – volume: 41 start-page: 375 year: 2012 ident: B31 article-title: The geographical distribution of yellow dwarf viruses and their aphid vectors in Australian grasslands and wheat. publication-title: Australas. Plant Pathol. doi: 10.1007/s13313-012-0133-7 – start-page: 290 year: 1990 ident: B53 article-title: Identification of the variants of Barley yellow dwarf virus in China publication-title: World perspectives on barley yellow dwarf – volume: 93 start-page: 242 year: 2011 ident: B3 article-title: Selective constraints, molecular recombination structure and phylogenetic reconstruction of isometric plant RNA viruses of the families Luteoviridae and Tymoviridae. publication-title: Biochemie doi: 10.1016/j.biochi.2010.09.017 – volume: 27 start-page: 221 year: 2010 ident: B9 article-title: SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msp259 – volume: 8 start-page: 1086 year: 2012 ident: B37 article-title: Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels. publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts094 – volume: 86 start-page: 370 year: 1996 ident: B4 article-title: Diversity among isolates within the PAV serotype of barley yellow dwarf virus. publication-title: Phytopathology doi: 10.1094/phyto-86-370 – start-page: 11 year: 1990 ident: B8 article-title: Current status of barley yellow dwarf in the United States: A regional situation report publication-title: World perspectives on barley yellow dwarf – volume: 168 start-page: 223 year: 2010 ident: B30 article-title: Detection of Cereal yellow dwarf virus using small interfering RNAs and enhanced rate with Cocksfoot streak virus in wild cocksfoot grass (Dactylis glomerata). publication-title: J. Virol. Methods doi: 10.1016/j.jviromet.2010.06.003 – start-page: 217 year: 1995 ident: B10 article-title: Biology and taxonomy of vectors of barley yellow dwarf viruses publication-title: Barley Yellow Dwarf: 40 Years of Progress – volume: 84 start-page: 6177 year: 2010 ident: B29 article-title: Long-term evolution of the Luteoviridae: time scale and mode of virus speciation. publication-title: J. Virol. doi: 10.1128/jvi.02160-09 – volume: 103 year: 2019 ident: B43 article-title: First report of wheat dwarf virus in winter wheat in Estonia. publication-title: Plant Dis. doi: 10.1094/PDIS-11-18-2059-PDN – volume: 9 year: 2018 ident: B36 article-title: Sensitivity of small RNA-based detection of plant viruses. publication-title: Front. Microbiol. doi: 10.3389/fmicb.2018.00939 – volume: 161 start-page: 551 year: 2016 ident: B14 article-title: Molecular diversity of turncurtoviruses in Iran. publication-title: Arch. Virol. doi: 10.1007/s00705-015-2686-6 – volume: 8 year: 2016 ident: B5 article-title: Characterization of a novel polerovirus infecting maize in China. publication-title: Viruses doi: 10.3390/v8050120 – volume: 6 start-page: 421 year: 1998 ident: B24 article-title: Getting a handle on RNA virus recombination. publication-title: Trends Microbiol. doi: 10.1016/s0966-842x(98)01384-5 – volume: 28 start-page: 341 year: 1990 ident: B23 article-title: Evolution and molecular biology of luteoviruses. publication-title: Annu. Rev. Phytopathol. doi: 10.1146/annurev.py.28.090190.002013 – volume: 3 start-page: 177 year: 2002 ident: B26 article-title: Barley yellow dwarf virus: Luteoviridae or Tombusviridae? publication-title: Mol. Plant Pathol. doi: 10.1046/j.1364-3703.2002.00112.x – volume: 6 year: 2011 ident: B48 article-title: Dynamics of molecular evolution and phylogeography of Barley yellow dwarf virus-PAV. publication-title: PLoS One doi: 10.1371/journal.pone.0016896 – start-page: 9 year: 1995 ident: B6 article-title: Symptomology and host range of barley yellow dwarf publication-title: Barley yellow dwarf: 40 years of progress – volume: 72 start-page: 1473 year: 1991 ident: B34 article-title: Use of group specific primers and the polymerase chain reaction for the detection and identification of luteoviruses. publication-title: J. Gen. Virol. doi: 10.1099/0022-1317-72-6-1473 – volume: 14 start-page: 179 year: 1995 ident: B25 article-title: Luteovirus gene expression. publication-title: Crit. Rev. Plant Sci. doi: 10.1080/713608119 – volume: 169 start-page: 211 year: 2010 ident: B52 article-title: Reverse transcription loop-mediated isothermal amplification of DNA for detection of barley yellow dwarf viruses in China. publication-title: J. Virol. Methods doi: 10.1016/j.jviromet.2010.06.020 – start-page: 337 year: 2003 ident: B12 article-title: Other cereals publication-title: Virus and Virus-like Diseases of Major Crops in Developing Countries doi: 10.1007/978-94-007-0791-7_13 – volume: 149 start-page: 843 year: 2004 ident: B2 article-title: Molecular diversity of the coat protein-encoding region of Barley yellow dwarf virus-PAV and Barley yellow dwarf virus-MAV from Latvia and Sweden. publication-title: Arch. Virol. doi: 10.1007/s00705-003-0242-2 – volume: 120 start-page: 69 year: 2004 ident: B21 article-title: Multiplexed RT-PCR for streamlined detection and separation of barley and cereal yellow dwarf viruses. publication-title: J. Virol. Methods doi: 10.1016/j.jviromet.2004.04.005 – volume: 10 start-page: 207 year: 2006 ident: B27 article-title: Molecular characterization of barley yellow dwarf virus coat protein gene in wheat and aphids. publication-title: Arab. J. Biotech. – volume: 1982 start-page: 381 year: 1982 ident: B35 article-title: Identification of barley yellow dwarf viruses: comparison of biological and serological methods. publication-title: Plant Dis. Rep. doi: 10.1094/pd-66-381 – volume: 148 start-page: 17 year: 2008 ident: B7 article-title: Development of a multiplexed PCR detection method for barley and cereal yellow dwarf viruses, wheat spindle streak virus, wheat streak mosaic virus and soil-borne wheat mosaic virus. publication-title: J. Virol. Methods doi: 10.1016/j.jviromet.2007.10.015 – volume: 110 start-page: 68 year: 2020 ident: B42 article-title: Sixty years after the first description: genome sequence and biological characterization of European wheat striate mosaic virus infecting cereal crops. publication-title: Phytopathology doi: 10.1094/PHYTO-07-19-0258-FI – volume: 56 start-page: 111 year: 2017 ident: B28 article-title: Barley yellow dwarf virus in barley crops in Tunisia: prevalence and molecular characterization. publication-title: Phytopathol. Mediterr. – volume: 152 start-page: 1365 year: 2007 ident: B19 article-title: A Chinese isolate of barley yellow dwarf virus-PAV represents a third distinct species within the PAV serotype. publication-title: Arch. Virol. doi: 10.1007/s00705-007-0947-8 – volume: 73 start-page: 2876 year: 1999 ident: B16 article-title: Primary and secondary structural elements required for synthesis of barley yellow dwarf virus subgenomic RNA1. publication-title: J. Virol. doi: 10.1128/jvi.73.4.2876-2885.1999 – volume: 161 start-page: 2047 year: 2016 ident: B51 article-title: The complete genomic sequence of a tentative new polerovirus identified in barley in South Korea. publication-title: Arch. Virol. doi: 10.1007/s00705-016-2881-0 – volume: 76 start-page: 2548 year: 2020 ident: B47 article-title: Identifying drivers of spatio−temporal dynamics in barley yellow dwarf virus epidemiology as a critical factor in disease control. publication-title: Pest Manag. Sci. doi: 10.1002/ps.5851 – volume: 154 start-page: 1125 year: 2009 ident: B50 article-title: The complete nucleotide sequence of the barley yellow dwarf GPV isolate from China shows that it is a new member of the genus Polerovirus. publication-title: Arch. Virol. doi: 10.1007/s00705-009-0415-8 – volume: 100 year: 2016 ident: B41 article-title: First report of brome mosaic virus in wheat in Estonia. publication-title: Plant Dis. doi: 10.1094/PDIS-04-16-0426-PDN – volume: 93 start-page: 1386 year: 2003 ident: B1 article-title: Barley yellow dwarf virus and cereal yellow dwarf virus quantification by real-time polymerase chain reaction in resistant and susceptible plants. publication-title: Virology doi: 10.1094/phyto.2003.93.11.1386 – volume: 241 start-page: 172 year: 2017 ident: B20 article-title: Crop-associated virus reduces the rooting depth of non-crop perennial native grass more than non-crop-associated virus with known viral suppressor of RNA silencing (VSR). publication-title: Virus Res. doi: 10.1016/j.virusres.2017.07.006 – volume: 8 year: 2013 ident: B44 article-title: Distribution of Barley yellow dwarf virus-PAV in the Sub-Antarctic Kerguelen Islands and characterization of two new Luteovirus species. publication-title: PLoS One doi: 10.1371/journal.pone.0067231 – volume: 19 start-page: 37 year: 2018 ident: B18 article-title: Optimized yellow dwarf virus multiplex PCR assay reveals a common occurrence of Barley yellow dwarf virus-PAS in Kansas winter wheat. publication-title: Plant Health Prog. doi: 10.1094/php-09-17-0056-rs – volume: 8 year: 2017 ident: B49 article-title: Identification, characterization and full-length sequence analysis of a novel polerovirus associated with wheat leaf yellowing disease. publication-title: Front. Microbiol. doi: 10.3389/fmicb.2017.01689 |
| SSID | ssj0000402000 |
| Score | 2.365202 |
| Snippet | Worldwide, barley/cereal yellow dwarf viruses (YDVs) are the most widespread and damaging group of cereal viruses. In this study, we applied high-throughput... |
| SourceID | doaj swepub pubmedcentral liege hal proquest crossref |
| SourceType | Open Website Open Access Repository Aggregation Database Enrichment Source Index Database |
| StartPage | 673218 |
| SubjectTerms | Agricultural Science Biotechnologie Biotechnology BYDV CYDV diagnostics epidemiology HTS Jordbruksvetenskap Life Sciences Luteovirus Microbiology Microbiology (medical) Mikrobiologi OYV Sciences du vivant wheat |
| Title | A Survey Using High-Throughput Sequencing Suggests That the Diversity of Cereal and Barley Yellow Dwarf Viruses Is Underestimated |
| URI | https://www.proquest.com/docview/2534614214 https://hal.inrae.fr/hal-04107128 https://orbi.uliege.be/handle/2268/291183 https://pubmed.ncbi.nlm.nih.gov/PMC8144474 https://res.slu.se/id/publ/112238 https://doaj.org/article/b44901dabaeb4b0cbfb08cf8853d0cfb |
| Volume | 12 |
| WOSCitedRecordID | wos000653629300001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVAON databaseName: DOAJ Open Access Full Text customDbUrl: eissn: 1664-302X dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0000402000 issn: 1664-302X databaseCode: DOA dateStart: 20100101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVHPJ databaseName: ROAD: Directory of Open Access Scholarly Resources customDbUrl: eissn: 1664-302X dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0000402000 issn: 1664-302X databaseCode: M~E dateStart: 20100101 isFulltext: true titleUrlDefault: https://road.issn.org providerName: ISSN International Centre |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1bi9NAFB50VfBFvGK8LKMIghhNJpPN5LF7Y4V1EVqlPg1ztYWQLknTpS-C_9xzJu3S-KAvltKEZCYNc05yvo9z-A4hb7CrkXDOxCbVKubK67gEHAF7AqI9sNys15k9Ly4uxHRaftlp9YU1Yb08cL9wHzXnELKs0spprhOjvU6E8QLCjE2M1_j2BdSzQ6bCOxhpUbJJYwILK8FMc6OBD7L0w0GRMWzysROIgl4_hJcZVkPeqjBfPYCcfxZMDmRFQyg6vU_ubTAkHfX3_oDccPVDcqfvKrl-RH6N6LhrVm5NQz0AxVKOeNL347nslnTcV0_jqXH3A_NLLZ3M1JICFqTH2zoNuvD0yAGkrKiqLT3ErPyafsdczRU9vlKNp9_mTde6ln5qaWifhIIdAICdfUy-np5Mjs7iTaeF2ACjwH70wuvcMqbynBmgMKnLs8SWotSJ8gmzGXwKo7n1XrlcGaE8WLMsSpezxGfZE7JXL2r3lFCLknoH2qVOF1ybTBSFFeApqS3hy31Eku2yS7ORIcduGJUEOoKWksFSEi0le0tF5N31lMteg-Nvgw_RltcDUT47HACnkhunkv9yqoi8Bk8YXONsdC7xWMKBMENQX6UReR8cBa6s53LFwrCw31XwV0ZqJwHcCskgoIgsIq-2_iThEca8jKrdomslyzMOKImlPCLFwNEGdzA8U89nQQxcACPmBcx827vkYEpbdVo1uJGtA7IHWFA8-x8L9JzcxTXHMoo0fUH2lk3nXpLbZrWct80-uVlMxX54IuH388-T38kzQNY |
| linkProvider | Directory of Open Access Journals |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=A+Survey+Using+High-Throughput+Sequencing+Suggests+That+the+Diversity+of+Cereal+and+Barley+Yellow+Dwarf+Viruses+Is+Underestimated&rft.jtitle=Frontiers+in+microbiology&rft.au=S%C3%B5mera%2C+Merike&rft.au=Massart%2C+S%C3%A9bastien&rft.au=Tamisier%2C+Lucie&rft.au=Soov%C3%A4li%2C+Pille&rft.date=2021-05-11&rft.pub=Frontiers+Media+S.A&rft.eissn=1664-302X&rft.volume=12&rft_id=info:doi/10.3389%2Ffmicb.2021.673218&rft_id=info%3Apmid%2F34046025&rft.externalDocID=PMC8144474 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1664-302X&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1664-302X&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1664-302X&client=summon |