Studi In-Silico: Identifikasi Tandem Repetitive Sequence Genom Ganoderma boninense Strain G3 sebagai Data Dasar Pengembangan Sistem Berbasis Data Molekuler Pengendalian Penyakit Busuk Pangkal Batang
In-Silico Study: Identification Of Tandem Repetitive Sequence On The Genome Of Ganoderma boninense Strain G3 As Fundamental Data For The Development Of Disease Management Of Basal Stem Rot Based On Molecular Data
DOI:
https://doi.org/10.21111/agrotech.v12i01.4Keywords:
Analisis in silico, Ganoderma boninense, penanda molekuler, tandem repetitive sequences, variabilitas genomAbstract
Analisis in silico telah dilakukan pada genom Ganoderma boninense strain G3 untuk mengidentifikasi tandem repetitive sequences (TRS) yang diketahui berperan penting dalam patogenisitas, plastisitas genom, dan adaptasi lingkungan. Sebanyak 5.176 TRS terdeteksi, dengan ukuran motif berkisar antara 1 hingga 285 bp serta menunjukkan variasi jumlah salinan yang cukup besar (1,8–52 salinan). Sebagian besar lokus menunjukkan konservasi sekuens internal yang tinggi, tercermin dari nilai kecocokan rata-rata sebesar 89,3% dan frekuensi indel median sebesar 0%, yang mengindikasikan bahwa lebih dari setengah lokus repeat tidak memiliki insersi maupun delesi, sehingga banyak susunan repeat yang tetap stabil secara struktural di bawah tekanan evolusi. Sebaliknya, sebagian kecil lokus memperlihatkan tingkat indel dan ekspansi repeat yang tinggi, menandakan keberadaan wilayah mirip minisatelit yang sangat bervariasi dan berpotensi dimanfaatkan sebagai penanda genotipe beresolusi tinggi. Nilai entropi yang umumnya tinggi (rata-rata 1,65) menunjukkan bahwa banyak motif TRS memiliki komposisi nukleotida yang seimbang. Secara keseluruhan, hasil ini mengungkap pola dan susunan TRS yang sangat beragam dalam G. boninense, yang bersifat konservatif maupun dinamis yang kemungkinan berkontribusi terhadap variabilitas genom. TRS yang sangat bervariasi ini merupakan kandidat untuk pengembangan penanda molekuler guna mendukung studi populasi, epidemiologi, dan ekologi pada patogen penting secara ekonomi ini.
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