Fig. 3

Basic process of chloroplast genetic engineering, diversity in intergenic spacer regions, and impact of transgene integration (endogenous versus heterologous genome sequences). a Complexity of heterologous sequence integration into intergenic spacer regions between lettuce and tobacco. The schematic diagram represents recombination between the tobacco transplastomic genome and the lettuce transformation vector [128]. Purple bars represent unique lettuce intron sequence; the green bar represents unique tobacco intron sequence; black bars are exon regions; blue regions are looped out sequence. The expression cassette comprises: promoters (P), leader sequence (L), gene of interest (GOI), terminators (T), and selectable marker gene (SMG). IG intergenic spacer region. b Basic process of chloroplast genetic engineering. Gene delivery is performed by bombardment with gold microparticles coated with chloroplast vectors, followed by three rounds of selection to achieve homoplasmy. After confirmation of transgene integration, plants are grown in the greenhouse to increase biomass. Chloroplast transgenes are maternally inherited without Mendelian segregation of introduced traits. c Comparison of 21 of the most variable intergenic spacer regions among Solanaceae chloroplast genomes. Atr Atropa, Pot potato, Tob tobacco, Tom tomato. *Tier 1, **tier 2, and ***tier 3 regions reported in the paper by Shaw et al. [250]. Plotted values were converted from percentage identity to sequence divergence on a scale from 0 to 1 as shown on the Y-axis; these values demonstrate a wide range of sequence divergence in different regions. Nucleotide sequences were determined by a bridging shotgun method and genome annotation was performed using the Dual Organellar GenoMe Annotator [13]. d, e Decrease in the expression of transgenes regulated by heterologous psbA promoters and untranslated regions (UTRs) engineered via tobacco chloroplast genomes. When the lettuce (La) psbA regulatory region was used in tobacco (Na) chloroplasts or vice versa, transgene expression is dramatically reduced. d Accumulation of a cholera toxin B subunit (CTB) and proinsulin (Pins) fusion protein (CP) was quantified by densitometry and e anthrax protective antigen (PA) accumulation was estimated by enzyme-linked immunosorbent assay (ELISA). Total leaf protein (TLP) or total soluble protein (TSP) data are presented as a function of light exposure and developmental stage. The order of young, mature, and old is different in d and e because of the accumulation of more CTB-Pins in older leaves and PA in mature leaves [128]. Young (top five), mature (fully grown), and old (bottom three) leaves were fully expanded and were cut from plants grown in the greenhouse for 8–10 weeks