Genomics of Avicennia marina grown near Karachi coast in Pakistan
Avicennia marina is a salt-tolerant mangrove species that dominates Pakistan's coastal ecosystems, yet no genome resource has previously been available for this population. Here, we report the first reference-guided de novo genome assembly and comprehensive annotation of A. marina from Pakistan. Illumina paired-end sequencing generated 160 million reads, producing a 446.6 Mb genome with a scaffold N50 of 14.2 Mb following SPAdes assembly and RagTag scaffolding. Iterative repeat masking revealed that 57.9% of the genome comprised repetitive elements, with Gypsy and Copia retrotransposons as the dominant classes. Using a combination of transcriptomic and protein homology evidence, we predicted 44,605 protein-coding genes with 92.7% BUSCO completeness. Functional annotation via BLASTp, InterProScan, and eggNOG-mapper assigned GO terms and KEGG pathways to over 29,000 genes, including hundreds implicated in salt stress and abscisic acid response. Comparative structural analysis using chromeister showed extensive synteny with the reference genome and revealed notable inversions and duplications, particularly on chromosome 26. Variant calling and structural variation analysis further identified genomic rearrangements contributing to local adaptation. This study provides the first genome-scale resource for A. marina from the Pakistan. These findings support future research in stress physiology, conservation genomics, and climate-adaptive breeding in halophytes.