Passifloraplastome sequencing reveals widespread genomic rearrangements

AbstractAlthough past studies have includedPassifloraamong angiosperm lineages with highly rearranged plastid genomes (plastomes), knowledge about plastome organization in the genus is limited. So far only one draft and one complete plastome have been published. Expanded sampling ofPassifloraplastomes is needed to understand the extent of the genomic rearrangement in the genus, which is also unusual in having biparental plastid inheritance and plastome‐genome incompatibility. We sequenced 15Passifloraplastomes using either Illumina paired‐end or shotgun cloning and Sanger sequencing approaches. Assembled plastomes were annotated using Dual Organellar GenoMe Annotator (DOGMA) and tRNAscan‐SE. ThePopulus trichocarpaplastome was used as a reference to estimate genomic rearrangements inPassifloraby performing whole genome alignment in progressiveMauve. The phylogenetic distribution of rearrangements was plotted on the maximum likelihood tree generated from 64 plastid encoded protein genes. Inverted repeat (IR) expansion/contraction and loss of the two largest hypothetical open reading frames,ycf1andycf2, account for most plastome size variation, which ranges from 139 262 base pairs (bp) inP. biflorato 161 494 bp inP. pittieri.Passifloraplastomes have experienced numerous inversions, gene and intron losses along with multiple independent IR expansions and contractions resulting in a distinct organization in each of the three subgenera examined. EachPassiflorasubgenus has a unique plastome structure in terms of gene content, order and size. The phylogenetic distribution of rearrangements shows thatPassiflorahas experienced widespread genomic changes, suggesting that such events may not be reliable phylogenetic markers.