Analisis Simple Sequence Repeats (SSR) dalam Genom Kloroplas Avicennia marina

Abstract

Avicennia marina is one of the primary mangrove species in Indonesia's coastal regions, known for its high salinity tolerance and strong potential in ecosystem rehabilitation efforts. To support the conservation and management of this species, a comprehensive understanding of its genetic diversity is essential. This study aims to identify and analyze Simple Sequence Repeats (SSR) motifs within the chloroplast genome of A. marina using an in silico approach. Chloroplast genome sequences were retrieved from the NCBI database and analyzed through a bioinformatics pipeline consisting of quality control, trimming, genome assembly, and SSR identification using MISA software. The results revealed a total of 137 SSR loci across a 148,263 bp chloroplast genome, with a strong dominance of adenine (A) and thymine (T) mononucleotide motifs. Most SSRs were located in non-coding regions of the genome, indicating their potential as effective molecular markers. This study highlights the relevance of chloroplast SSRs for genetic and conservation research in mangrove species and provides a foundation for the development of specific primers to support more adaptive mangrove rehabilitation strategies.