Table 2. Correlation of Nonreference TE Insertions in the Resequenced Genomes with Accumulated TEs in the Reference Genome
Whole ChromosomesChromosomal Arms
Features comparedarbPcrbPc
Densities of nonreference LTR-RTs: G. max versus G. soja0.778<10−40.669<10−4
Densities of nonreference LTR-RTs/copia: G. max versus G. soja0.581<10−40.563<10−4
Densities of nonreference LTR-RTs/gypsy: G. max versus G. soja0.754<10−40.526<10−4
Densities of nonreference DNA TEs: G. max versus G. soja0.286<10−40.187<10−4
Densities of nonreference LTR-RTs in G. max versus proportions of accumulated LTR-RTs0.707<10−40.497<10−4
Densities of nonreference LTR-RTs/copia in G. max versus proportions of accumulated LTR-RTs/copia0.466<10−40.309<10−4
Densities of nonreference LTR-RTs/gypsy in G. max versus proportions of accumulated LTR-RTs/gypsy0.630<10−40.468<10−4
Densities of nonreference DNA TEs in G. max versus proportions of accumulated DNA TE DNA−0.1140.00040.0210.6874
Densities of nonreference LTR-RTs in G. soja versus proportions of accumulated LTR-RTs0.864<10−40.712<10−4
Densities of nonreference LTR-RTs/copia in G. soja versus proportions of accumulated LTR-RTs/copia0.681<10−40.494<10−4
Densities of nonreference LTR-RTs/gypsy in G. soja versus proportions of accumulated LTR-RTs/gypsy0.793<10−40.760<10−4
Densities of nonreference DNA TEs in G. soja versus proportions of accumulated DNA TE DNA−0.239<10−4−0.0230.6553
  • a Density refers to numbers of nonreference TE insertions per 1-Mb region, and proportion refers to percentage of TE DNA in each 1-Mb region.

  • b Pearson correlation coefficient.

  • c All P values calculated by 10,000 bootstrap resamplings.