Fig. 4

Pipeline of Sunset-specific genomic integration of nuclear organelle DNA fragments. a. Alignment between Sunset reads and organelle reference genome. Unmapped reads were removed after subsequent analysis. Soft-clipped reads were shown in the red box, which refers to reads with mismatches at the extremities. b. Extraction of reads with at least 5 bp mismatches (≥5 bp) at the extremities. c. de novo assembly of norgDNA by SOAPdenovo. d. Extraction of reliable Sunset norgContigs. Only blast hits of norg contigs with ≥30 bp mapped to organelle genomes and ≥ 5 bp unmatched on the edges were considered as reliable norgContigs. e. Junction sites specific in Sunset. The Sunset-specific norg sequences were obtained when no hits were determined using BLAST against the SunUp reference genome. f. Identity between the six organelle-like borders of transgenic insertions in SunUp and Sunset norgDNA