Analysis of Chloroplast and Mitochondrial DNA Insertions in the Nucleus (Nupts and Numts)

Supplemental Figures:

Figure S1. Distribution of NUPTs and NUMTs on the twelve chromosomes of rice. The length of the vertical lines indicates the length of the NUPT/NUMT, the color indicates its nucleotide divergence from organellar DNA. The coverage of the chromosome by different TE families measured as the proportion of TEs in sliding window is visualized for each chromosome.

Figure S2. Distribution of NUPTs on the nineteen chromosomes of grapevine. The length of the vertical lines indicates the length of the NUPT/NUMT, the color indicates its nucleotide divergence from organellar DNA. The coverage of the chromosome by different TE families measured as the proportion of TEs in sliding window is visualized for each chromosome.

Figure S3. Distribution of NUPTs and NUMTs on the ten chromosomes of sorghum. The length of the vertical lines indicates the length of the NUPT/NUMT, the color indicates its identity with cpDNA. The coverage of the chromosome by different TE families measured as the proportion of TEs in sliding window is visualized for each chromosome.

Figure S4. Distribution of NUPTs on the twenty chromosomes of soybean. The length of the vertical lines indicates the length of the NUPT, the color indicates its nucleotide divergence from organellar DNA. The coverage of the chromosome by different TE families measured as the proportion of TEs in sliding window is visualized for each chromosome.

Figure S5. Distribution of NUPTs and NUMTs on the ten chromosomes of maize. The length of the vertical lines indicates the length of the NUPT/NUMT, the color indicates its nucleotide divergence from organellar DNA. The coverage of the chromosome by different TE families measured as the proportion of TEs in sliding window is visualized for each chromosome.

Figure S6. The distance of neighboring NUPTs or NUMTs in organellar genome plotted against their distance in nucleus in maize. In Figure (a) we calculated neighboring NUPTs in the same orientation in plastid genome (first column) or irrespective of their orientation (second column), differing in divergence at most by 5% and 10% (first and second row, respectively), interrupted by intervening sequence formed mostly by TEs (90% coverage by TEs). In Figure (b) same analysis for NUMTs is presented.

Table S1. Sources of data. The databases and accession numbers of plastid, mitochondrial and nuclear genomes of plant species used in our study.

Table S2. Genomic coordinates of identified NUPTs and NUMTs. Filters described in Materials and Methods section were applied.