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All Journal Gontor AGROTECH Science Journal Jurnal Perlindungan Tanaman Indonesia Jurnal Ilmiah Pertanian Caraka Tani: Journal of Sustainable Agriculture Agricultural Science
Adyatma Irawan Santosa
Department Of Plant Protection, Faculty Of Agriculture, Universitas Gadjah Mada
Agriculture, Biological Sciences & Forestry Education

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A Survey of Phytopathogenic Fungi and Oomycetes in Riyadh, Saudi Arabia Arya Widyawan; Boy Valenza Damiri; Adyatma Irawan Santosa; Haris Setyaningrum
Gontor AGROTECH Science Journal Vol 1, No 2 (2015): Juni 2015
Publisher : University of Darussalam Gontor, Ponorogo, East Java Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21111/agrotech.v1i2.261

Abstract

A survey of phytopathogenic fungi and Oomyceteswas conducted in Riyadh, Kingdom of Saudi Arabia duringOctober 2008 – May 2009. Total of 223 samples were collectedfrom four regions; Al-Kharj, Oyaynah, Old Diriyah, and Al Amariyah. Isolation was done using Potato Dextrose Agar(PDA). Infected parts were cut then sterilized in chlorox(10%), then were put in petridish that contain PDA andincubated at 25-27 °C. A total twelve genera of fungi andsingle genera of Oomycetes were isolated from the infectedplants and identifi ed as Fusarium spp., Alternaria spp.,Helmintosphorium (Bipolaris) spp., Sclerotium spp., Rhizoctoniaspp., Cladosporium spp., Mauginiella scattae, Erysiphe spp.,Leveillula spp., Macrophomina phaseolina, Ustilago spp.,Ulocladium spp., and Phytium spp.
Cross amplification of 16S rRNA bacterial primer 27F/1492R on horticultural crop chloroplast genome Santosa, Adyatma Irawan; Hilmany, Taufiq; Dewi, Nurul Aulia; Rahmawati, Novianti Ekaputri; Putri, Erika Ananda; Hafidsya, Tiara; Setyaningrum, Ary Virgianti; Dewi, Rulia Ervina; Sari, Gracela Nanda Puspita; Nubatonis, Mars Buwn Fraset Manao; Widyawan, Arya
Agricultural Science Vol. 7 No. 2 (2024): March
Publisher : Faculty of Agriculture, Merdeka University Surabaya, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55173/agriscience.v7i2.132

Abstract

Molecular techniques have been applied as fast and accurate detection methods of plant pathogenic bacteria. Bacteria-specific primer 27F paired with the universal primer 1492R was used in PCR to detect plant pathogenic bacteria in symptomatic leaves of tomato (Solanum lycopersicum L.), chili pepper (Capsicum annum L.), napa cabbage (Brassica rapa subsp. pekinensis L.), cabbage (Brassica oleracea var. capitata L.), and longan (Dimocarpus longan Lour.). The targeted single bands with length of 1400 bp were obtained but bidirectional sequencing of the PCR products recovered partial sequence of chloroplast instead of bacterial genomes. Thus, this result confirmed cross amplification of 27F/1492R primer pair against chloroplast genome of plants. Phylogenetic tree was constructed to separate the tested isolates according to their taxonomic relations: Order Sapindales, Solanales, and Brassicales. In-silico analysis on the new five and nineteen selected sequences in NCBI GenBank detected at least seven conserved regions with some single nucleotide polymorphisms. This report might be a cautionary advice for other researchers to avoid false positive results which could lead to misdiagnosis of bacterial plant diseases.
Molecular Characterization of Mungbean yellow mosaic India virus and Tomato leaf curl New Delhi virus in Sukoharjo and Magelang Regencies, Indonesia Surwadinata, Antama; Putro, Ananda Restu; Pradhana, Adhi; Shalihah, Filzah; Pancasona, Muhammad Garda; Saputra, Rachmad; Haj Ali, Mayadah A.; Santosa, Adyatma Irawan
Jurnal Perlindungan Tanaman Indonesia Vol 29, No 1 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jpti.101371

Abstract

Diseases caused by Begomoviruses in black-eyed pea (Vigna unguiculata subsp. unguiculata) and cucumber (Cucumis sativus) are remains insufficiently explored in Indonesia. One symptomatic black-eyed pea and two cucumber samples were collected from Sukoharjo and Magelang Regencies, respectively, to be molecularly tested using Krusty/Homer and SPG1/SPG2 primer pairs for universal detection of Begomoviruses. NCBI BLAST analysis on the obtained nucleotide sequences confirmed mungbean yellow mosaic India virus (MYMIV, Begomovirus vignaradiataindiaense) infection in black-eyed pea sample and tomato leaf curl New Delhi virus (ToLCNDV, Begomovirus solanumdelhiense) infection in both cucumber samples. Sequences of partial AV1, and partial AC1 and AC2 genes of the three isolates were registered with accession nos. PQ539469-71 and PQ539476-78, respectively, in NCBI GenBank. No recombination signal was detected in the sequences of the new isolates according to scan by Recombination Detection Program (RDP v.5.30). In the phylogenetic trees built by MEGA 11 software with Tamura-Nei parameter model, MYMIV H-2 as well as ToLCNDV N-8 and V-97 isolates shared basal nodes with Indonesian isolates, indicated their close genetic relationship with other isolates also found in the country. While expanding our information regarding genetic diversity of Begomoviruses, this study also reported the first cases of MYMIV in black-eyed pea in Indonesia and ToLCNDV in cucumber in Magelang, to the best of our knowledge.
Updates on hosts and distribution of pepper yellow leaf curl Indonesia virus and squash leaf curl China virus in Central Java Province, Indonesia Santosa, Adyatma Irawan; Irbati, Adenisa Hanifah; Pratiwi, Geby Nandita Cahyaning; Surwadinata, Antama; Laeshita, Putri; Dharma, Krisnanda Surya; Jaya, Reko Saputra; Andriyani, Annisa Lisa; A'yun, Chilya Qurrota; Fatika, Chusnu Naura Syifa
Jurnal Ilmiah Pertanian Vol. 21 No. 1 (2024): Jurnal Ilmiah Pertanian
Publisher : Universitas Lancang Kuning

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31849/jip.v21i1.18856

Abstract

Chili pepper, tomato, and squash cultivated in Magelang Regency, Central Java Province, Indonesia showed severe viral symptoms. Three samples were taken then molecularly tested against begomovirus, potyvirus, tobamovirus, and polerovirus. However, PCR test confirmed only begomovirus infections. BLAST analysis concluded that the chili pepper and tomato isolates were pepper yellow leaf curl Indonesia virus (PepYLCIV) while the squash isolate was squash leaf curl China virus (SLCCNV). The 552 bp partial AV1 gene sequences of the three isolates were given NCBI GenBank acc nos. OR924278-80. PepYLCIV OR924279 and OR924280 formed a subgroup with LC542629 from Bali in the phylogenetic tree constructed using MEGA11, and shared 95.8 – 96.7% identities at nucleotide (nt) and 98.4 – 99.5% at amino acid (aa) levels according to Sequence Demarcation Tool v1.2 software. Meanwhile, SLCCNV OR924278 was clustered, and shared 95.8 – 96.7% nt and 98.4 – 99.5% aa identities with three Malaysian isolates (MW248685, MW248687, and MW248689). Different plant species inoculated with SLCCNV OR924278 remained symptomless up to four weeks observation, suggesting that the isolate is not mechanically transmissible. This study contributed additional knowledge on molecular variation while expanding hosts and distribution of PepYLCIV and SLCCNV in Central Java Province.
Molecular Identification of Three Potyviruses Infecting Allium cepa var. aggregatum and Allium sativum in Central Cultivation Areas of Indonesia Santosa, Adyatma Irawan; Nasir, Muh Amat; Çelik, Ali; Farooq, Tahir; Subiastuti, Aprilia Sufi
Caraka Tani: Journal of Sustainable Agriculture Vol 39, No 2 (2024): October
Publisher : Universitas Sebelas Maret

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20961/carakatani.v39i2.86146

Abstract

One hundred and twenty shallot (Allium cepa var. aggregatum) and 22 garlic (Allium sativum) samples were collected from major growing regions and markets to determine the distribution and molecular diversity of 3 potyviruses: leek yellow stripe virus (LYSV), onion yellow dwarf virus (OYDV), and shallot yellow stripe virus (SYSV) in Indonesia. The results of reverse transcription-polymerase chain reaction (RT-PCR) showed that 83% of shallot and all garlic samples were infected by at least 1 virus species. Coat protein (CP) region of 8 Indonesian LYSV, 19 OYDV, and 10 SYSV isolates were sequenced and given accession nos. OR772038-OR772082 in NCBI GenBank. Five isolates were recombinants according to analysis using the Recombination Detection Program (RDP v5.30). The phylogenetic tree deduced that 6 LYSV Indonesian and 2 China imported isolates belong to S-type. All tested OYDV isolates, including the 19 isolates, were clustered separately according to their respective hosts: onion and garlic. The 10 Indonesian SYSV isolates were clustered together in the same group and thus shown to be closely related. All isolates tested in this study were estimated to be still within their respective species demarcation according to percentage identity analysis. This was the most comprehensive molecular study on LYSV, OYDV, and SYSV that may help to find sustainable management strategies according to conditions in Indonesia and contribute to the global knowledge on the genetic diversity of the 3 viruses.
Potato Virus Y and Shallot Latent Virus of Kajoran Horticultural Production Center, Magelang Regency, Indonesia: Molecular Characterization Case Study Santosa, Adyatma Irawan; Irbati, Adenisa Hanifah; Dharma, Krisnanda Surya; Winona, Belinda; Jaya, Reko Saputra; Andriyani, Annisa Lisa; A'yun, Chilya Qurrota
Caraka Tani: Journal of Sustainable Agriculture Vol 39, No 1 (2024): April
Publisher : Universitas Sebelas Maret

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20961/carakatani.v39i1.76737

Abstract

Kajoran Sub-district is a horticultural production center that supplies horticultural commodities for Central Java Province, especially Magelang. However, plant viral diseases of Kajoran have not been studied. This paper aimed to identify plant viral diseases in this horticultural production center. Some samples were taken: three potatoes (Solanum tuberosum) and three shallots (Allium cepa var. aggregatum), then tested respectively with RT-PCR, using two pairs of universal primers to detect Potyvirus and Carlavirus. The result showed two potato samples were infected by Potyvirus (potato virus Y/PVY) and three shallot samples by Carlavirus (shallot latent virus/SLV). GenBank accession no. OR180052 to OR180056 were assigned to the obtained partial sequences of the five isolates. The phylogenetic analysis makes the two new PVY Indonesian isolates in strain N group thus confirmed the presence of the first PVYN in Indonesia. The constructed SLV phylogenetic tree clusters the new three isolates with eight shallot isolates in a group and separated it from isolates from other plant species. The tested PVY isolates shared 95.2 to 100% nucleotide identities among them, while 78.9 to 98.5% identities were estimated among compared SLV isolates. This study expands our understanding of the genetic variation of PVY and SLV in Indonesia, potentially leading us to find the perfect management for the viruses.
Co-Authors A'yun, Chilya Qurrota Andriyani, Annisa Lisa Arya Widyawan Arya Widyawan, Arya Boy Valenza Damiri Çelik, Ali Dewi, Nurul Aulia Dewi, Rulia Ervina Dharma, Krisnanda Surya Farooq, Tahir Fatika, Chusnu Naura Syifa Hafidsya, Tiara Haj Ali, Mayadah A. Haris Setyaningrum Hilmany, Taufiq Irbati, Adenisa Hanifah Jaya, Reko Saputra Nasir, Muh Amat Nubatonis, Mars Buwn Fraset Manao Pancasona, Muhammad Garda Pradhana, Adhi Pratiwi, Geby Nandita Cahyaning Putri Laeshita, Putri Putri, Erika Ananda Putro, Ananda Restu Rahmawati, Novianti Ekaputri Saputra, Rachmad Sari, Gracela Nanda Puspita Setyaningrum, Ary Virgianti Shalihah, Filzah Subiastuti, Aprilia Sufi Surwadinata, Antama Winona, Belinda