Fig. 3

Pipeline of SunUp-specific genomic integration of nuclear organelle DNA fragments. a. Quality control of raw sequenced data. b. Searches for SunUp nuclear organelle junction sites by BLASTN [25]. The BLASTN algorithm was used to search SunUp genome for nuclear plastid DNA (NUPT) and nuclear mitochondria DNA (NUMT) integrations with papaya organelle genomes as databases. Only hits with ≥30 bp mapped to organelle genomes were considered. c. Alignment between Sunset reads and SunUp reference genome. Unmapped reads were removed after subsequent analysis. d. Nuclear organelle junction sites shared by SunUp and Sunset. A junction site was supposed to be shared by SunUp and Sunset genomes when there were reads mapped to and spanning its position in the SunUp reference genome. e. Extraction of reliable shared junction sites. The mixture of reads that aligned back to the reference genome may originate from different sources of DNA in the Sunset genome, including nuclear DNA (nuDNA), nuclear organelle DNA (norgDNA) and organelle DNA (orgDNA). In order to discriminate these three categories of reads and extract the reliable junction sites shared by SunUp and Sunset, the flanking regions (5 bp upstream and downstream) of the junction sites are used as an indicator. Reliable norgDNA reads were selected if those reads were spanning the junction sites and mapped to at least 5 bp of norgDNA or nuDNA. f. Junction sites specific in SunUp. If there were no reads mapped to or no reliable norgDNA reads spanning the junction site, we considered this junction site as a SunUp-specific norgDNA junction site