Ni Putu Sri Asih, Risha Amilia Pratiwi, Istiana Prihatini, Paramita Cahyaningrum Kuswandi, Evy Yulianti, Arief Priyadi
Pinanga arinasae is an endangered species endemic to Bali, Indonesia. The aims of our study are to characterize its chloroplast genome through comparison with other chloroplast genomes, including its phylogenetic position within the subfamily Arecoideae and to identify potential molecular markers. P. arinasae chloroplast genome characterization involves Illumina-based sequencing, de novo genome assembly, gene annotation, amino acid frequency and codon usage pattern analysis, and simple sequence marker (SSR) identification. Comparative analysis was conducted on phylogenetic tree reconstruction, comparison of amino acid frequency, codon usage pattern, SSR number, inverted repeat junction arrangement, genome length, GC content, and gene number. The calculation of nucleotide diversity relates to the identification of substitution markers. The complete circular chloroplast genome of P. arinasae was found to be 156,773 bp in length, and exhibited 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 found to be 37.41%. A total of 130 genes were annotated, including 85 protein-coding, eight rRNA, and 37 tRNA genes. Leucine was found to be the most frequent amino acid, and tryptophan the least abundant. The AGA codon was found to have the highest relative synonymous codon usage value. No significant gene rearrangements were found in P. arinasae when compared to other members of the subfamily Arecoideae. Phylogenetic analysis revealed that P. arinasae was a 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. The chloroplast genome of P. arinasae has been characterized and compared within the subfamily Arecoideae. All the above findings help bridge gaps in knowledge relating to palm phylogenetics, while the molecular markers generated have the potential to serve as cost-effective tools for the assessment of genetic diversity and the provision of support for future conservation efforts and sustainable utilization of P. arinasae. © TÜBİTAK.
Herbarium Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Bogor, Indonesia; Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, Indonesia; Department of Biology Education, Faculty of Mathematics and Natural Sciences, Universitas Negeri Yogyakarta, Sleman, Yogyakarta, Indonesia
