The complete plastome of Passiflora cirrhiflora A. Juss.: structural features, RNA editing sites, hotspots of nucleotide diversity and molecular markers within the subgenus Deidamioides

Abstract

The family Passifloraceae contains approximately 1000 species distributed in 36 genera. Passiflora, a species-rich genus, is divided into five subgenera: Astrophea, Decaloba, Deidamioides, Passiflora, and Tetrapathea. Passiflora cirrhiflora A. Juss. (subgenus Deidamioides) is an Amazonian species occurring in North Brazil, Venezuela, Guiana, Suriname, and French Guiana. Plastomes of the subgenus Deidamioides have demonstrated a complex pattern of evolution concerning phylogenetic aspects, size, rearrangements, gene losses, and pseudogenization. Therefore, we completely sequenced the plastome of P. cirrhiflora and characterized it in detail. The P. cirrhiflora plastome is a DNA molecule of 163,365 bp and contains 109 unique genes (75 protein-coding genes, 30 tRNAs, and 4 rRNAs). The infA and rps7 are pseudogenes in P. cirrhiiflora and the loss of the rps16 and rpl22 genes is a common feature shared by all plastomes of the genus Passiflora sequenced to date. Comparative analyses revealed a considerable structural variation at the IR borders, which consequently affected plastome size and structure within the subgenus Deidamioides. According to our prediction analysis, RNA editing sites are highly conserved within the subgenus Deidamioides, which significantly differs from the subgenus Passiflora. A total of 230 SSRs and six hotspots of nucleotide polymorphism were detected in the plastome of P. cirrhiiflora. Taken together, the complete plastome sequence of P. cirrhiflora is useful data for several studies in different areas such as phylogeny, genetic, and evolution.