Comparative analysis of the complete chloroplast genome of the rare endemic palm Pinanga arinasae Witono from Bali, Indonesia

Background/aim: Pinanga arinasae is an endangered species endemic to Bali, Indonesia. Our study aims to characterize its chloroplast genome, compare it with other chloroplast genomes, including its phylogenetic position within the Arecoideae subfamily, and identify potential molecular markers. Materials and methods: P. arinasae chloroplast genomes characterization involves Illumina-based sequencing, de novo genome assembly, gene annotation, amino acid frequency, codon usage pattern analysis, and Simple Sequence Marker (SSR) identification. Comparative analysis include phylogenetic tree reconstruction, comparison of amino acid frequency, codon usage pattern, SSR number, inverted repeat junction arrangement, genome length, GC content, and gene number. Nucleotide diversity is calculated to identify substitution markers. Results: The complete circular chloroplast genome of P. arinasae was 156,773 bp in length, exhibiting a quadripartite structure that consisted of a pair of 25,853 bp inverted repeats, an 18,337 bp small single-copy region, and an 86,730 bp large single-copy region. The overall GC content was 37,41%. A total of 130 genes were annotated, including 85 protein-coding, eight rRNA, and 37 tRNA genes. Leucine was the most frequent amino acid, while tryptophan was the least abundant. The AGA codon had the highest relative synonymous codon usage value. Despite minor expansions and contractions in the inverted repeats, no significant gene rearrangements were found in P. arinasae when compared to other Arecoideae subfamily. Phylogenetic analysis revealed that P. arinasae was sister species with P. Coronata. Additionally, 98 simple sequence repeats and mutational hotspot regions, such as trnS-GCU—trnS-CGA, trnD-GUC— trnY-GUA, psbC—trnS-UGA, petA-psbJ, and rpl32—trnL-UAG were identified as molecular markers. Conclusion: The chloroplast genome of Pinanga arinasae has been characterized and compared within the Arecoideae subfamily. These findings help bridge knowledge gaps in palm phylogenetics. The molecular markers generated can serve as cost-effective tools for assessing genetic diversity and offer support for future conservation efforts and sustainable utilization of P. arinasae.