Table 2.

A Brief Summary of Results on Fate of Missing or Divergent Plastid Genes with Transcriptome Analyses.

Gene	Description	Gene Status in Passiflora Plastome	Transcriptome Results
rpl20	Ribosomal protein L20, 50S subunit	Missing in subgenera Passiflora and Decaloba. P. pittieri contains premature stop codon. Present in all species in Deidamioides and P. tetrandra	Putatively substituted by a duplicated nuclear-encoded mitochondrial rpl20
rpl22	Ribosomal protein L22, 50S subunit	Missing in all Passiflora species including Adenia Mannii, species from a genus sister to Passiflora	Functional transfer to a nuclear gene containing RNA recognition motif
rpl32	Ribosomal protein L32, 50S subunit	Missing in P. pittieri (Astrophea), P. contracta + P. obovata (Deidamioides), P. jatunsachensis + P. rufa + P. auriculata + P. filipes + P. misera + P. affinis + P. biflora (Decaloba)	Transfer to the duplicated copy of nuclear chloroplastic Cu–Zn dismutase gene
rps7	Ribosomal protein S7, 30S subunit	Missing in P. obovata (Deidamioides) and in subgenus Decaloba except P. microstipula	Functional transfer into the intron of nuclear thioredoxin (m type) gene
rps16	Ribosomal protein S16, 30S subunit	Missing in all Passiflora species including outgroup genus Populus	Substituted by dual-targeted nuclear-encoded mitochondrial gene
ycf1/ycf2	Components of TIC and motor protein complexes	Missing in subgenera Decaloba and Passiflora expect in species P. microstipula and P. foetida	No nuclear transcript identified. Potentially substituted by alternative TIC and motor protein complexes
rpoA	RNA polymerase subunit alpha	Highly divergent gene in subgenus Decaloba	No nuclear transcript identified. The divergent plastid rpoA remain potentially functional