Genetic Diversity of <i>Amylomyces rouxii</i> from <i>Ragi tapai</i> in Java Island Based on Ribosomal Regions ITS1/ITS2 and D1/D2

<i>Amylomyces rouxii</i> is commonly found as amylolytic fungi in <i>tapai</i> fermentation. However, its diversity is rarely reported despite being often used for food production in Southeast Asia. This research aims to analyze the genetic diversity and the distribution pattern of <i>A</i>. <i>rouxii</i> from <i>Ragi tapai</i> in Java Island, Indonesia. We isolated the fungus from samples obtained from <i>Ragi tapai</i> producing centers in Bandung, Sumedang, Muntilan, Blora, Yogyakarta, and Bondowoso. The obtained isolates were molecularly identified based on the ribosomal regions ITS1/ITS2 and D1/D2, then analyzed for phylogenetic tree reconstruction, genetic distance, genetic variation, and haplotype networking. Six isolates showed specific morphological traits of <i>A. rouxii</i>. However, phylogenetic tree reconstruction on the ribosomal genes showed that the isolates were grouped into two different clades related to two species. Clade A included BDG, SMD, and MTL isolates related to <i>A</i>. <i>rouxii,</i> whereas clade B included YOG, BLR, and BDS isolates related to <i>Mucor indicus.</i> The genetic distances between clades for ITS1/ITS2 and D1/D2 were 0.6145 and 0.1556, respectively. In conclusion, we confirmed the genetic diversity of molds from <i>Ragi tapai</i> in Java Island and showed that the isolates are not only related to <i>A. rouxii</i> as reported before.