Evaluation of Krusty/Homer and SPG1/SPG2 Primer Pairs in Identification of Six Begomoviruses Commonly Found in Indonesia

Nabilla Kurnialaili Defitra; Hayu Alifia Zahra; Antama Surwadinata; Rachmad Saputra; Aprilia Sufi Subiastuti; Mayadah A. Haj Ali; Adyatma Irawan Santosa

doi:10.22146/jtbb.15670

Nabilla Kurnialaili Defitra Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Sleman 55281, Indonesia https://orcid.org/0009-0007-5934-9927
Hayu Alifia Zahra Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Sleman 55281, Indonesia https://orcid.org/0009-0004-3066-5983
Antama Surwadinata Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Sleman 55281, Indonesia https://orcid.org/0009-0008-3117-3314
Rachmad Saputra Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Sleman 55281, Indonesia; Plant Protection Study Program, Agrotechnology Department, Agriculture Faculty, Universitas Riau, Kota Pekanbaru 28293, Indonesia https://orcid.org/0000-0003-1837-2956
Aprilia Sufi Subiastuti Laboratory of Microbiology, Faculty of Biology, Universitas Gadjah Mada, Sleman 55281, Indonesia https://orcid.org/0000-0003-2456-8744
Mayadah A. Haj Ali Department of Plant Pathology, International Centre for Agricultural Research in the Dry Areas (ICARDA), Cairo 11728, Egypt; Department of Microbiology and Immunology, National Commission for Biotechnology (NCBT), Damascus, Syria https://orcid.org/0000-0003-3225-7348
Adyatma Irawan Santosa Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Sleman 55281, Indonesia https://orcid.org/0000-0002-2826-5444

DOI: https://doi.org/10.22146/jtbb.15670

Keywords: Molecular variation, PCR, Phylogenetic tree, Plant DNA virus, Plant viral disease

Abstract

Fourteen symptomatic crops and weeds from Magelang, Klaten, Sleman, and Bantul Regencies were tested against begomoviruses using Krusty/Homer and SPG1/SPG2 primer pairs. The acquired nucleotide sequences were involved in phylogenetic analysis which clustered isolates into six species. Furthermore, three recombinant isolates were also identified. Protocol for molecular characterization of prevalent begomoviruses using both primer pairs was initiated in this report. Molecular data of the obtained 14 isolates added important information on the genetic diversity of Indonesian isolates.

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