Genetika Evolusioner pada Spesies Salacca Berdasarkan Genom Kloroplas, Gen, dan Keanekaragaman Urutan Intergenik

Abstract

This thesis explores the chloroplast genomes (Cp) and sequence diversity of key genomic regions in seven Salacca species, commonly known as snake fruit. The initial analysis involves constructing and examining Cp genomes using data from the BGISeq-500 platform and GetOrganelle assemblers, revealing a consistent structure across genomes with lengths varying between 157,047 and 158,182 kilobase pairs. A detailed comparative genomics analysis identifies the ycf1 gene as having the highest number of single nucleotide polymorphisms (SNPs), with significant findings such as missing amino acids in Salacca affinis and a prevalence of mononucleotide SSR motifs. Additionally, variability in the junctions of large single copy (LSC), inverted repeat (IR), and small single copy (SSC) regions is noted, particularly in S. wallichiana. The study further investigates the sequence diversity of the rbcL, matK, ITS, trnL-F, and atpH-F regions, employing Sanger sequencing and gene-specific primers to address species identification challenges due to morphological similarities and complex taxonomy. The development of 26 Single Nucleotide Amplified Polymorphism (SNAP) primers shows high specificity and efficiency, facilitating precise species identification. Phylogenetic analysis reveals that the Salacca species form distinct clades with a recent common ancestor, emphasizing their close evolutionary relationships. This research highlights the utility of Cp genome information and specific genomic regions in advancing our understanding of genetic diversity, species identification, evolutionary biology, and conservation efforts within the Salacca genus. The findings establish a genetic connection between Salacca and Cocos nucifera and highlight the contrast with Phoenix dactylifera, providing crucial insights for future studies and breeding programs.