Blastn v2.11.0 + [63 (link)] was used to identify transfer events from organelles to the nuclear genome with the filter parameter ‘identity greater than 80% and alignment length greater than 100 bp’. These results were further divided into two datasets: 80–89% and 90–100% similarity to a known organelle sequence to represent older (more mutations) and newer (fewer mutations) transfers respectively. In addition, each dataset was further divided into different length categories of 100–199 bp, 200–299 bp, 300–399 bp, 400–499 bp, 500–599 bp, 600–699 bp, 700–799 bp, 800–899 bp, 900–999 bp, and 1000 bp and above. BEDtools v2.30.0 [71 (link)] was used to annotate organelle transfer locations in the nuclear genome and their distribution patterns in different chromosomes and genomic regions (i.e. exon, intron, intergenic, mRNA) based on the annotation file of the nuclear genome. The transfer fragment and the 5’ and 3’ flanking sequences (100–499 bp, 500–1000 bp, and above 1000 bp) were extracted and calculated for GC content. The program ggplot2 v3.3.6 [72 (link)] was used for visualization.
Free full text: Click here
