Molecular characterization of a Bean common mosaic virus isolate inciting severe symptoms on yardlong bean in Gunungkidul Regency, Indonesia.

Rossa Wulandari, Ida Afifatun Nisa', Aulia Diva Surya Putri, Alyah Shufa, Ummu Azhizah Nuraini, Septiana Septiana, Efriandi Efriandi, Adhyatma Noor Rizal, Adyatma Irawan Santosa

Abstract


In 2023, an outbreak of viral disease on yardlong bean (Vigna unguiculata ssp. sesquipedalis) was reported in Tanjungsari District of Gunungkidul Regency, Indonesia. Symptomatic leaves showing mosaic, chlorosis, severe blistering, and leaf malformation were collected as a composite sample and then molecularly tested with RT-PCR. The sample was positive for potyvirus infection using U341/Poty1 universal primer pair, and BLAST analysis on the obtained nucleotide sequence further specified bean common mosaic virus (BCMV, Potyvirus phaseovulgaris) as the causal agent of the disease. Sequence of 691 bp of 3’-end region of BCMV-GKD-Ida isolate was registered in NCBI GenBank with accession no. PZ118702. The phylogenetic tree constructed using the Maximum Likelihood method with Tamura 3-parameter substitution model clustered BCMV-GKD-Ida with other BCMV isolates from 17 countries but in a distinct monophyletic branch. A paired identity analysis using the Sequence Demarcation Tool (SDT) software version 1.3 estimated that BCMV-GKD-Ida shares a fairly low nucleotide identity of 86.5%-92.5% with the compared BCMV isolates, further indicating considerable genetic variation. BCMV is one of most important plant pathogens that threaten the productivity legumes. This research provides additional molecular data and contributes a basis for early diagnosis and control strategies for the virus in yardlong bean.

Keywords


Fabaceae; Nucleotide identity; Phylogenetic tree; Plant virus; RT-PCR;

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DOI: https://doi.org/10.21107/agrovigor.v19i2.34067

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Copyright (c) 2026 Rossa Wulandari, Ida Afifatun Nisa', Aulia Diva Surya Putri, Alyah Shufa, Ummu Azhizah Nuraini, Septiana Septiana, Efriandi Efriandi, Adhyatma Noor Rizal, Adyatma Irawan Santosa