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

Abstract

An in silico analysis was conducted on the genome of Ganoderma boninense strain G3 to identify tandem repeat sequences (TRSs), which are known to play important roles in pathogenicity, genome plasticity, and environmental adaptation. A total of 5.176 TRSs were detected, spanning motif sizes ranging from 1 to 285 bp and displaying substantial variation in copy number (1.8–52 copies). Most loci exhibited high internal sequence conservation, as reflected by an average nucleotide match of 89.3% and a median indel frequency of 0%, indicating that many repeat arrays remain structurally stable and may be maintained by functional or evolutionary constraints. In contrast, a subset of loci showed elevated indel levels and pronounced repeat expansions, suggesting the presence of hypervariable minisatellite-like regions with potential utility for high-resolution genotyping. Entropy values were generally high (mean 1.65), signifying that many TRS motifs possess balanced nucleotide compositions rather than simple low-complexity repeats. Collectively, these findings reveal a structurally diverse TRS landscape in G. boninense strain G3 encompassing both conserved and dynamic repeat families that likely contribute to genomic variability. The identified hypervariable TRSs represent promising candidates for the development of molecular markers to support population, epidemiological, and ecological studies of this economically important pathogen.