Molecular Characterization of Hovenia Dulcis-Associated Virus 1 (HDaV1) and 2 (HDaV2): New Tentative Species within the Order <i>Picornavirales</i>
In a systematic field survey for plant-infecting viruses, leaf tissues were collected from trees showing virus-like symptoms in Brazil. After viral enrichment, total RNA was extracted and sequenced using the MiSeq platform (Illumina). Two nearly full-length picorna-like genomes of 9534 and 8158 nucl...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-08-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/12/9/950 |
| _version_ | 1797555433299247104 |
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| author | Flávia M. B. Nery Fernando L. Melo Leonardo S. Boiteux Simone G. Ribeiro Renato O. Resende Anelise F. Orílio Josiane G. Batista Mirtes F. Lima Rita C. Pereira-Carvalho |
| author_facet | Flávia M. B. Nery Fernando L. Melo Leonardo S. Boiteux Simone G. Ribeiro Renato O. Resende Anelise F. Orílio Josiane G. Batista Mirtes F. Lima Rita C. Pereira-Carvalho |
| author_sort | Flávia M. B. Nery |
| collection | DOAJ |
| description | In a systematic field survey for plant-infecting viruses, leaf tissues were collected from trees showing virus-like symptoms in Brazil. After viral enrichment, total RNA was extracted and sequenced using the MiSeq platform (Illumina). Two nearly full-length picorna-like genomes of 9534 and 8158 nucleotides were found associated with <i>Hovenia dulcis</i> (<i>Rhamnaceae</i> family). Based upon their genomic information, specific primers were synthetized and used in RT-PCR assays to identify plants hosting the viral sequences. The larger contig was tentatively named as <i>Hovenia dulcis</i>-associated virus 1 (HDaV1), and it exhibited low nucleotide and amino acid identities with <i>Picornavirales</i> species. The smaller contig was related to insect-associated members of the <i>Dicistroviridae</i> family but exhibited a distinct genome organization with three non-overlapping open reading frames (ORFs), and it was tentatively named as <i>Hovenia dulcis</i>-associated virus 2 (HDaV2). Phylogenetic analysis using the amino acid sequence of RNA-dependent RNA polymerase (RdRp) revealed that HDaV1 and HDaV2 clustered in distinct groups, and both viruses were tentatively assigned as new members of the order <i>Picornavirales</i>. HDaV2 was assigned as a novel species in the <i>Dicistroviridae</i> family. The 5′ ends of both viruses are incomplete. In addition, a nucleotide composition analysis (NCA) revealed that HDaV1 and HDaV2 have similarities with invertebrate-infecting viruses, suggesting that the primary host(s) of these novel virus species remains to be discovered. |
| first_indexed | 2024-03-10T16:46:26Z |
| format | Article |
| id | doaj.art-ffe697231a9a47c9872442e20bb5dbe7 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T16:46:26Z |
| publishDate | 2020-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-ffe697231a9a47c9872442e20bb5dbe72023-11-20T11:35:07ZengMDPI AGViruses1999-49152020-08-0112995010.3390/v12090950Molecular Characterization of Hovenia Dulcis-Associated Virus 1 (HDaV1) and 2 (HDaV2): New Tentative Species within the Order <i>Picornavirales</i>Flávia M. B. Nery0Fernando L. Melo1Leonardo S. Boiteux2Simone G. Ribeiro3Renato O. Resende4Anelise F. Orílio5Josiane G. Batista6Mirtes F. Lima7Rita C. Pereira-Carvalho8Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília DF 70910-900, BrazilDepartamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília DF 70910-900, BrazilEmbrapa Hortaliças, Brasília DF 70275-970, BrazilEmbrapa Recursos Genéticos e Biotecnologia, Brasília DF 70770-017, BrazilDepartamento de Biologia Celular, Campus Universitário Darcy Ribeiro, Universidade de Brasília (UnB), Brasília DF 70910-900, BrazilDepartamento de Biologia Celular, Campus Universitário Darcy Ribeiro, Universidade de Brasília (UnB), Brasília DF 70910-900, BrazilDepartamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília DF 70910-900, BrazilEmbrapa Hortaliças, Brasília DF 70275-970, BrazilDepartamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília DF 70910-900, BrazilIn a systematic field survey for plant-infecting viruses, leaf tissues were collected from trees showing virus-like symptoms in Brazil. After viral enrichment, total RNA was extracted and sequenced using the MiSeq platform (Illumina). Two nearly full-length picorna-like genomes of 9534 and 8158 nucleotides were found associated with <i>Hovenia dulcis</i> (<i>Rhamnaceae</i> family). Based upon their genomic information, specific primers were synthetized and used in RT-PCR assays to identify plants hosting the viral sequences. The larger contig was tentatively named as <i>Hovenia dulcis</i>-associated virus 1 (HDaV1), and it exhibited low nucleotide and amino acid identities with <i>Picornavirales</i> species. The smaller contig was related to insect-associated members of the <i>Dicistroviridae</i> family but exhibited a distinct genome organization with three non-overlapping open reading frames (ORFs), and it was tentatively named as <i>Hovenia dulcis</i>-associated virus 2 (HDaV2). Phylogenetic analysis using the amino acid sequence of RNA-dependent RNA polymerase (RdRp) revealed that HDaV1 and HDaV2 clustered in distinct groups, and both viruses were tentatively assigned as new members of the order <i>Picornavirales</i>. HDaV2 was assigned as a novel species in the <i>Dicistroviridae</i> family. The 5′ ends of both viruses are incomplete. In addition, a nucleotide composition analysis (NCA) revealed that HDaV1 and HDaV2 have similarities with invertebrate-infecting viruses, suggesting that the primary host(s) of these novel virus species remains to be discovered.https://www.mdpi.com/1999-4915/12/9/950viromemetagenomics<i>Hovenia dulcis</i>HDaV1HDaV2<i>Picornavirales</i> |
| spellingShingle | Flávia M. B. Nery Fernando L. Melo Leonardo S. Boiteux Simone G. Ribeiro Renato O. Resende Anelise F. Orílio Josiane G. Batista Mirtes F. Lima Rita C. Pereira-Carvalho Molecular Characterization of Hovenia Dulcis-Associated Virus 1 (HDaV1) and 2 (HDaV2): New Tentative Species within the Order <i>Picornavirales</i> Viruses virome metagenomics <i>Hovenia dulcis</i> HDaV1 HDaV2 <i>Picornavirales</i> |
| title | Molecular Characterization of Hovenia Dulcis-Associated Virus 1 (HDaV1) and 2 (HDaV2): New Tentative Species within the Order <i>Picornavirales</i> |
| title_full | Molecular Characterization of Hovenia Dulcis-Associated Virus 1 (HDaV1) and 2 (HDaV2): New Tentative Species within the Order <i>Picornavirales</i> |
| title_fullStr | Molecular Characterization of Hovenia Dulcis-Associated Virus 1 (HDaV1) and 2 (HDaV2): New Tentative Species within the Order <i>Picornavirales</i> |
| title_full_unstemmed | Molecular Characterization of Hovenia Dulcis-Associated Virus 1 (HDaV1) and 2 (HDaV2): New Tentative Species within the Order <i>Picornavirales</i> |
| title_short | Molecular Characterization of Hovenia Dulcis-Associated Virus 1 (HDaV1) and 2 (HDaV2): New Tentative Species within the Order <i>Picornavirales</i> |
| title_sort | molecular characterization of hovenia dulcis associated virus 1 hdav1 and 2 hdav2 new tentative species within the order i picornavirales i |
| topic | virome metagenomics <i>Hovenia dulcis</i> HDaV1 HDaV2 <i>Picornavirales</i> |
| url | https://www.mdpi.com/1999-4915/12/9/950 |
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