Chloroplast genome sequence of Pandanus odorifer (Forssk.) Kuntze: genome features, mutational hotspots and phylogenetic analyses

Pandanus odorifer (Forssk.) Kuntze commonly called as Kewda (Pandanaceae) is an important aromatic plant, most celebrated for its unique fragrance and the only native species representing subgenus Pandanus in India. In this study, chloroplast genome sequence of P. odorifer was sequenced for the first time and compared with the closely allied Pandanus species P. tectorius as well as other Pandanales members to understand gene content and structural variations. The size of complete plastome was 1,57,885 bp, with Large Single Copy (85,947 bp), Small Single Copy (18,112 bp) and a pair of Inverted Repeats, IRs (26,913 bp). The plastome exhibited total 133 genes, 82 protein coding genes and 19 genes duplicated in IR region. The multiple sequence alignment of all Pandanales plastomes exhibited conserved nature. The plastome of P. odorifer also showed truncated rps19, full length rpoC2 and unique RNA editing site which differentiated it from the closely allied P. tectorius plastome. The highest nucleotide diversity was found in ndhF and ycf4-cemA regions of P. odorifer and P. tectorius. The plastome of Pandanus exhibited conserved nature when compared to Pandanales plastomes, except an inversion leading to cemA-petA regions in Stemona plastomes. The phylogenetic analysis based on complete plastome and protein coding genes placed P. odorifer and P. tectorius as sister species.