Molecular characterization of the MXMT gene involved in caffeine biosynthesis in Liberica coffee (Coffea liberica Hiern) from East Java, Indonesia

The methylxanthine methyltransferase (MXMT) gene encodes key enzyme in the caffeine biosynthesis of Coffea species. This study analyzed a 175 bp MXMT gene fragment from Coffea liberica collected in Wonosalam, East Java, Indonesia, and compared it with homologous sequences from related Coffea taxa retrieved from GenBank. BLAST analysis showed identical sequence 100 % between the East Java accession and C. liberica var. dewevrei, indicating strong conservation within the liberica group. Phylogenetic reconstruction using the Neighbor-Joining (NJ) method clustered C. liberica East Java with C. liberica var. dewevrei, while C. canephora formed a separate branch, indicating distinct MXMT fragment sequence. Sequence comparisons identified missense mutation among species, primarily in comparisons with C. canephora. Despite sequence polymorphisms, all accessions shared full query coverage (100 %), confirming the conserved structure of the MXMT region. Overall, these results suggest that the analyzed MXMT fragment can differentiate in C. liberica from other Coffea species, but more samples are needed to clarify the variation.