Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia

Abstract. Harti H, Hidayat SH, Sobir, Wiyono S. 2020. Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia. Biodiversitas 21: 1697-1701. Research was conducted to identify main viruses infecting shallot in several...

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Autores principales:	Heri Harti, SRI HENDRASTUTI HIDAYAT, SOBIR, SURYO WIYONO
Formato:	article
Lenguaje:	EN
Publicado:	MBI & UNS Solo 2020
Materias:	diba, nib gene, phylogenetic tree, sequence analysis, sequence homology Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/0ea2c77180e6469a987c695a14235ec5
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spelling	oai:doaj.org-article:0ea2c77180e6469a987c695a14235ec52021-11-22T00:34:39ZDetection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia1412-033X2085-472210.13057/biodiv/d210451https://doaj.org/article/0ea2c77180e6469a987c695a14235ec52020-03-01T00:00:00Zhttps://smujo.id/biodiv/article/view/5400https://doaj.org/toc/1412-033Xhttps://doaj.org/toc/2085-4722Abstract. Harti H, Hidayat SH, Sobir, Wiyono S. 2020. Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia. Biodiversitas 21: 1697-1701. Research was conducted to identify main viruses infecting shallot in several regions in Indonesia and to further characterize genetic variation of Onion yellow dwarf virus (OYDV). Field survey was conducted in Central Java (Brebes), East Java (Probolinggo), West Sumatera (Alahan Panjang), West Nusa Tenggara (Bima), and South Sulawesi (Enrekang). Virus detection from field samples was conducted by dot immunobinding assay. This detection confirmed that infection of OYDV, Shallot yellow stunt virus (SYSV), Shallot latent virus (SLV), and Garlic common latent virus (GarCLV) has occurred in all field with incidence ranged from 20 to 93.5%, 2 to 93%, 21.5 to 80%, and 2 to 80.5%, respectively. The specific primers of Nib gene successfully amplified DNA fragments of OYDV from all locations. Sequencing of DNA fragments revealed that the amplified product was 351 bp. Sequence analysis indicated that the present OYDV isolates from Indonesia shared homology from 82 to 95%; and they had homology from 81 to 95% with OYDV isolates from other countries. The similarity of OYDV isolates from different geographical locations reflected the movements of seed bulbs among and within countries. The phylogenetic tree also revealed that OYDV isolates from different countries did not group together indicating their diverse origin.Heri HartiSRI HENDRASTUTI HIDAYATSOBIRSURYO WIYONOMBI & UNS Soloarticlediba, nib gene, phylogenetic tree, sequence analysis, sequence homologyBiology (General)QH301-705.5ENBiodiversitas, Vol 21, Iss 4 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	diba, nib gene, phylogenetic tree, sequence analysis, sequence homology Biology (General) QH301-705.5
spellingShingle	diba, nib gene, phylogenetic tree, sequence analysis, sequence homology Biology (General) QH301-705.5 Heri Harti SRI HENDRASTUTI HIDAYAT SOBIR SURYO WIYONO Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia
description	Abstract. Harti H, Hidayat SH, Sobir, Wiyono S. 2020. Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia. Biodiversitas 21: 1697-1701. Research was conducted to identify main viruses infecting shallot in several regions in Indonesia and to further characterize genetic variation of Onion yellow dwarf virus (OYDV). Field survey was conducted in Central Java (Brebes), East Java (Probolinggo), West Sumatera (Alahan Panjang), West Nusa Tenggara (Bima), and South Sulawesi (Enrekang). Virus detection from field samples was conducted by dot immunobinding assay. This detection confirmed that infection of OYDV, Shallot yellow stunt virus (SYSV), Shallot latent virus (SLV), and Garlic common latent virus (GarCLV) has occurred in all field with incidence ranged from 20 to 93.5%, 2 to 93%, 21.5 to 80%, and 2 to 80.5%, respectively. The specific primers of Nib gene successfully amplified DNA fragments of OYDV from all locations. Sequencing of DNA fragments revealed that the amplified product was 351 bp. Sequence analysis indicated that the present OYDV isolates from Indonesia shared homology from 82 to 95%; and they had homology from 81 to 95% with OYDV isolates from other countries. The similarity of OYDV isolates from different geographical locations reflected the movements of seed bulbs among and within countries. The phylogenetic tree also revealed that OYDV isolates from different countries did not group together indicating their diverse origin.
format	article
author	Heri Harti SRI HENDRASTUTI HIDAYAT SOBIR SURYO WIYONO
author_facet	Heri Harti SRI HENDRASTUTI HIDAYAT SOBIR SURYO WIYONO
author_sort	Heri Harti
title	Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia
title_short	Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia
title_full	Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia
title_fullStr	Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia
title_full_unstemmed	Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia
title_sort	detection of major viruses infecting shallot and molecular characterization of onion yellow dwarf virus from several locations in indonesia
publisher	MBI & UNS Solo
publishDate	2020
url	https://doaj.org/article/0ea2c77180e6469a987c695a14235ec5
work_keys_str_mv	AT heriharti detectionofmajorvirusesinfectingshallotandmolecularcharacterizationofonionyellowdwarfvirusfromseverallocationsinindonesia AT srihendrastutihidayat detectionofmajorvirusesinfectingshallotandmolecularcharacterizationofonionyellowdwarfvirusfromseverallocationsinindonesia AT sobir detectionofmajorvirusesinfectingshallotandmolecularcharacterizationofonionyellowdwarfvirusfromseverallocationsinindonesia AT suryowiyono detectionofmajorvirusesinfectingshallotandmolecularcharacterizationofonionyellowdwarfvirusfromseverallocationsinindonesia
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Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia

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