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Plant Diversity and Resources

Passiflora plastome sequencing reveals widespread genomic rearrangements

Samar O. Rabah1†, Bikash Shrestha2*†, Nahid H. Hajrah3, Mumdooh J. Sabir4, Hesham F. Alharby1, Mernan J. Sabir1, Alawiah M. Alhebshi3, Jamal S. M. Sabir3, Lawrence E. Gilbert2, Tracey A. Ruhlman2, and Robert K. Jansen2,3

1Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia

2Department of Integrative Biology, University of Texas at Austin, Austin TX 78712, USA

3Center of Excellence for Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Saudi Arabia

4Department of Information Technology, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, 21589, Saudi Arabia

Keywords: homoplasy, inversion, IR expansion and contraction, Passifloraceae, plastome, rearrangement.


Although past studies have included Passiflora among 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 of Passiflora plastomes 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 15 Passiflora plastomes 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.  The Populus trichocarpa plastome was used as a reference to estimate genomic rearrangements in Passiflora by 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, ycf1 and ycf2, account for most plastome size variation, which ranges from 139 262 base pairs (bp) in P. biflora to 161 494 bp in P. pittieriPassiflora plastomes 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.  Each Passiflora subgenus has a unique plastome structure in terms of gene content, order and size.  The phylogenetic distribution of rearrangements shows that Passiflora has experienced widespread genomic changes, suggesting that such events may not be reliable phylogenetic markers.

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