Complete Chloroplast Genome of Indonesian Sugarcane (Saccharum ‘Bululawang’): Comparative, Structural, and Evolutionary Analysis of Photosystem I-Encoding Genes

Abstract

Sugarcane is one of the most important crops, providing the majority of global sugar production and serving as a major feedstock for bioenergy. Increasing demands for sustainable sugar production under climate and productivity constraint have intensified the need for molecular-level characterization of elite cultivars. Indonesia, as a country with a long history of sugarcane cultivation, has several superior sugarcane cultivars. The domestic sugarcane ‘Bululawang’ is currently dominant due to its advantageous agronomic parameters. Molecular investigations, particularly genome sequencing and functional analysis of photosystem I, are essential to understand the mechanisms underlying photosynthesis and biomass formation. This study aimed to perform comparative plastome analysis of sugarcane ‘Bululawang’ against other species from Saccharum and Zea; and specifically characterise the psa genes in terms of gene organization, protein structure and codon usage bias. Methods included sample collection, high molecular weight DNA isolation, library preparation, long-read sequencing, chloroplast genome assembly and annotation, followed by gene classification and data analysis. The analysis covered comparative chloroplast genome analysis, phylogenetic and selection pressure analysis, gene structure, conserved motifs, protein structure and codon usage bias analysis. The results showed that the plastome of Saccharum ‘Bululawang’ exhibited high conservation across species within Saccharum genus. The concatenated sequences provided sufficient phylogenetic resolution at the genus level. Each of the five photosystem I-encoding genes feature a single-exon structure without introns and possess highly conserved functional motifs (p-value 2.29 × 10⁻⁵⁵ to 0.00 × 10⁰). Protein analysis revealed high stability (ipTM > 0.95) in PsaA and PsaB subunits, with structural similarity nearly identical to the reference (RMSD < 1.0 Å). Codon usage profiling indicated a bias towards TTA (RSCU 3.01) and CGG (RSCU 3.00) codons. In conclusion, sugarcane ‘Bululawang’ possesses a conserved photosystem I structure, warranting further investigation into its functional relevance for photosynthetic efficiency.