| dc.description.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. | |
