Tiara Putria Judith 1, Aliyah Syahidah 1, Denianto Agung Wicaksono 1, Muhammad Anjas Zulfikar 1, Kah Ooi Chua 2 and Ganies Riza Aristya 1*
1Laboratory of Genetics and Breeding, Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; 2Centre for Research in Biotechnology for Agriculture (CEBAR) & Institute of Biological Sciences (ISB), Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
*Corresponding author: ganies_riza@ugm.ac.id
Sugarcane (Saccharum spp. hybrid) is a major tropical C4 crop with high sucrose productivity, sustained by efficient photosynthesis occurring within the chloroplasts. Plastid-encoded RNA polymerase (PEP), encoded by the rpo gene family (rpoA, rpoB, rpoC1 and rpoC2), plays a key role in chloroplast gene expression. Despite the agronomic importance of elite Indonesian sugarcane such as ‘Kidang Kencana’ and ‘Bululawang’, specific genomic information on the chloroplast rpo gene family is still lacking. In this study, we performed an integrative analysis of the rpo gene family to evaluate the genomic characteristics, structural conservation and evolutionary relationships. Long-read sequencing yielded approximately 8.0 Gb of data, enabling the assembly of complete circular chloroplast genomes with an average sequencing depth of 178.6×. The assembled chloroplast genomes were deposited in GenBank under accession numbers PZ344155 (‘Kidang Kencana’) and PZ364438 (‘Bululawang’), providing the reference sequences for comparative analyses of the rpo gene family. The four rpo genes were identified as single-copy, intronless genes located in the LSC region, ranging in length from 1,020 bp (rpoA) to 4,605 bp (rpoC2). Protein motif analysis identified 30 conserved motifs (p‐values ≤2.12×10-158), while codon usage patterns were highly similar between cultivars (ΔRSCU = −0.57 to 0.36), indicating conserved translational preferences. Predicted protein structures exhibited high prediction confidence (pLDDT >90) with low structural divergence. Phylogenetic analysis produced a well-supported topology (ML = 100%, BI = 1.00), clearly resolving the evolutionary relationships among the analyzed Saccharum taxa. These findings expand genomic resources for Indonesian sugarcane and provide a foundation for future evolutionary studies and chloroplast marker development.