Table 2. Correlation of Nonreference TE Insertions in the Resequenced Genomes with Accumulated TEs in the Reference Genome.

	Whole Chromosomes		Chromosomal Arms
Features compareda	rb	Pc	rb	Pc
Densities of nonreference LTR-RTs: G. max versus G. soja	0.778	<10−4	0.669	<10−4
Densities of nonreference LTR-RTs/copia: G. max versus G. soja	0.581	<10−4	0.563	<10−4
Densities of nonreference LTR-RTs/gypsy: G. max versus G. soja	0.754	<10−4	0.526	<10−4
Densities of nonreference DNA TEs: G. max versus G. soja	0.286	<10−4	0.187	<10−4
Densities of nonreference LTR-RTs in G. max versus proportions of accumulated LTR-RTs	0.707	<10−4	0.497	<10−4
Densities of nonreference LTR-RTs/copia in G. max versus proportions of accumulated LTR-RTs/copia	0.466	<10−4	0.309	<10−4
Densities of nonreference LTR-RTs/gypsy in G. max versus proportions of accumulated LTR-RTs/gypsy	0.630	<10−4	0.468	<10−4
Densities of nonreference DNA TEs in G. max versus proportions of accumulated DNA TE DNA	−0.114	0.0004	0.021	0.6874
Densities of nonreference LTR-RTs in G. soja versus proportions of accumulated LTR-RTs	0.864	<10−4	0.712	<10−4
Densities of nonreference LTR-RTs/copia in G. soja versus proportions of accumulated LTR-RTs/copia	0.681	<10−4	0.494	<10−4
Densities of nonreference LTR-RTs/gypsy in G. soja versus proportions of accumulated LTR-RTs/gypsy	0.793	<10−4	0.760	<10−4
Densities of nonreference DNA TEs in G. soja versus proportions of accumulated DNA TE DNA	−0.239	<10−4	−0.023	0.6553

^aDensity refers to numbers of nonreference TE insertions per 1-Mb region, and proportion refers to percentage of TE DNA in each 1-Mb region.

^bPearson correlation coefficient.

^cAll P values calculated by 10,000 bootstrap resamplings.