Karakterisasi Molekuler dan Variasi Genetik Isolat Begomovirus Berdasarkan Sekuens Parsial DNA-A dari Tanaman Hortikultura di Kabupaten Jember, Sleman, dan Temanggung

Aulia Robiatul Adawiyah, Dr. Aprilia Sufi Subiastuti, S.Si.

2026 | Skripsi | BIOLOGI

Begomovirus merupakan kelompok virus tanaman yang memiliki keragaman genetik tinggi dan dapat menginfeksi berbagai tanaman inang budidaya. Penelitian ini bertujuan untuk mengidentifikasi Begomovirus yang menginfeksi tanaman timun (Cucumis sativus), terung (Solanum melongena), dan tembakau (Nicotiana tabacum) berdasarkan analisis sekuens parsial DNA-A, menganalisis variasi genetik dan hubungan kekerabatan antarisolat, serta menganalisis adanya indikasi rekombinasi genetik. Sampel tanaman timun, terung, dan tembakau bergejala dikoleksi dari Kab. Jember, Kab. Sleman, dan Kab. Temanggung. Kemudian dilakukan deteksi menggunakan primer SPG1/SPG2 dan sekuensing Sanger. Sekuens yang diperoleh dianalisis menggunakan BLAST, Sequence Demarcation Tool, analisis filogenetik, dan Recombination Detection Program. Hasil penelitian menunjukkan bahwa isolat timun Sleman (TM) memiliki kesamaan tertinggi sebesar 96,74?ngan Begomovirus solanumdelhiense (ToLCNDV), isolat terung Jember (T1) sebesar 98,86?n terung Temanggung (T2) sebesar 98,73?ngan Begomovirus solanumflavuskanchanaburiense (TYLCKaV), sedangkan isolat tembakau Temanggung (TK) sebesar 97?ngan Begomovirus cucurbitachinaense (SLCCV). Variasi genetik ditunjukkan oleh perbedaan tingkat kemiripan nukleotida dan pola pengelompokan filogenetik antarisolat. Analisis rekombinasi menunjukkan satu sinyal potensial pada isolat TK pada wilayah nukleotida 372-864 yang didukung oleh metode MaxChi (p = 1,704 x 10^-2) dan SiScan (p = 4,622 x 10^-6), tetapi belum cukup kuat untuk mengonfirmasi terjadinya peristiwa rekombinasi. 

Begomovirus is a group of plant viruses characterized by high genetic diversity and the ability to infect various cultivated host plants. This study aimed to identify Begomovirus infecting cucumber (Cucumis sativus), eggplant (Solanum melongena), and tobacco (Nicotiana tabacum) based on partial DNA-A sequence analysis, investigate genetic variation and phylogenetic relationships among isolates, and assess potential evidence of genetic recombination. Symptomatic cucumber, eggplant, and tobacco samples were collected from Jember, Sleman, and Temanggung Regencies, Indonesia. Virus detection was performed using the SPG1/SPG2 primers, followed by Sanger sequencing. The obtained sequences were analyzed using BLAST, the Sequence Demarcation Tool, phylogenetic analysis, and the Recombination Detection Program (RDP). The results showed that the cucumber isolate from Sleman (TM) exhibited the highest nucleotide identity of 96.74% with Begomovirus solanumdelhiense (ToLCNDV), while the eggplant isolates from Jember (T1) and Temanggung (T2) showed nucleotide identities of 98.86% and 98.73%, respectively, with Begomovirus solanumflavuskanchanaburiense (TYLCKaV). Meanwhile, the tobacco isolate from Temanggung (TK) exhibited 97% nucleotide identity with Begomovirus cucurbitachinaense (SLCCV). Genetic variation was indicated by differences in nucleotide identity levels and phylogenetic clustering patterns among isolates. Recombination analysis identified one potential recombination signal in isolate TK within the nucleotide region 372–864, supported by the MaxChi (p = 1.704 × 10?²) and SiScan (p = 4.622 × 10??) methods. However, the evidence was insufficient to confirm the occurrence of a recombination event.

Kata Kunci : Begomovirus, DNA-A parsial, keragaman genetik, rekombinasi genetik, analisis filogenetik.