Deciphering the complete chloroplast genome sequence of Prain: Insights into genome structure, comparative analysis and phylogenetic relationship.

In the present study, we have characterized the complete chloroplast (Cp) genome of Prain (family Papaveraceae), revealing the plastome size of 153,290 bp, and a GC content of 38.72 %. The cp genome features the typical circular quadripartite structure found in flowering plants, including a pair of inverted repeat regions (25,816 bp), isolated by a small single-copy region (17,740 bp) and a large single-copy (83,918 bp). Genome annotation revealed 132 genes: 87 protein-coding genes, 37 tRNAs and eight rRNAs. This comparative study demonstrated that the genome structure, gene number and GC ratio are consistent with several other cp genomes of and genera. A total of 120 SSRs were detected in the plastome, the majority (111) of which were mononucleotide repeats. Among the longer repeats, palindromic sequences were most common, followed by forward, reverse, and complement repeats. The whole genome alignment revealed the conserved nature of the inverted repeat region over single-copy zones. Nucleotide diversity unveiled hypervariable sites (, , , and ) in both the small and large single-copy regions, which could be useful for designing molecular markers for taxonomic identification. Phylogenetic analysis revealed a close alliance of with other species, such as and , with strong bootstrap support. Molecular dating suggests that originated during the Tortonian age of the Miocene epoch of the Cenozoic era. These findings provide valuable insights for biological research, especially in understanding the genetic and evolutionary divergence within the Papaveraceae family.