Whole Genome Assembly, Annotation, and Comparative Genomic Analysis of Pandanus amaryllifolius

The genome assembly of Pandanus amaryllifolius, a plant renowned for its culinary and medicinal uses, has been successfully completed. The assembled genome size is approximately 494 Mb, closely aligning with the estimated 509 Mb determined by flow cytometry. Chromosome analysis confirmed a diploid chromosome number of 2n = 60. The assembly encompasses a total contig length of approximately 494.1 Mb, across 1448 contigs, and demonstrates significant contiguity with an N50 of 9.02 Mb and an N90 of 512 kb. The largest contig extends over 32.4 Mb, contributing to an average contig length of 341 kb. BUSCO analysis further underscores the assembly’s quality, with 96.05% of the gene models being complete or fragmented and 94.42% of them being complete. Genome annotation identified that non-long terminal repeat (LTR) sequences constitute 4.46% of the genome, LTR sequences make up 30.79%, and DNA transposons account for 2.46%, with transposable elements collectively making up 46.97% of the genome. Phylogenetic analysis positioned P. amaryllifolius closely related to Musa acuminata within the monocot lineage. This comprehensive genome assembly of P. amaryllifolius enhances the existing genomic resources and provides a foundation for future research and breeding programs.