Figure 1.
The circular map of the mitochondrial genome of G. max.
Features on the clockwise- and counter-clockwise-transcribed strands are drawn on the inside and outside of the circle, respectively. The figure was drawn using OGDraw v1.2 [65].
Figure 2.
Relationships revealed by multiple alignments among five R1 large repeats (marked as R1a–e).
R1b, R1d, R1e are in the some orientation; R1a and R1c are in the reverse orientation. The red segments S6* in R1b and R1c are homologous, but different from S6 in the other three R1 large repeats.
Table 1.
Locations of large repeats R1 and homologous sequences in the soybean mitochondrial genome.
Table 2.
Location of the large repeats (R2–R4) in the soybean mitochondrial genome.
Figure 3.
Reversible reorganization of the soybean mtDNA may produce multiple subgenomic circles mediated by large repeats.
(A) Arrows of the same color denote homologous large repeats and their sequence orientation. (B) shows subgenomic circles of various sizes produced by rearrangements of the five pairs of large repeats. (C) The three small circles may be produced by three pairs of large repeats (R1b-R1d, R1d-R1e and R1b-R1e).
Figure 4.
Isometric genome structures formed by rearrangements within eight pairs of inverted large repeats.
(A) is structurally the same as Figure 3A. (B–I) shows the eight isometric master genome structures of (A). The red arrows in the circles denote the inverted regions mediated by the repeats. Combinations of inverted repeats for each isometric master circle are marked in the circles.
Figure 5.
Chromosome coverage of hits obtained by searching the mitochondrial genome against the nuclear assembly.
Rectangles show the lengths of matches covering the chromosomes. The lines show percent coverage by the matches on the soybean chromosomes.
Figure 6.
Characteristics of nuclear-mitochondrial sequences in soybean.
Results are based on a BLAST e-value cutoff of 1e–12. (A) Distributions of percent identities between shared nuclear-mitochondrial matches. The number of matches is shown by brown boxes and is plotted on the left ordinate. The red and blue square lines show the coverage of matches on nuclear and mitochondrial genomes, respectively, and are plotted on the right ordinate. (B) Distributions of lengths between shared nuclear-mitochondrial matches; the notation method is the same as for (A).
Figure 7.
Phylogeny of four Faboideae mitochondrial genomes.
Numbers above each node represent bootstrap values from 1000 replicates. Branch lengths are in units of synonymous substitutions per synonymous site.
Table 3.
Features of the soybean mitochondrial genome.
Figure 8.
DNA transfers among the nuclear, chloroplast and mitochondrial genomes in soybean.
Figure 9.
Phylogenetic tree of representative mitochondrial genomes in higher plants.
Phylogenetic trees were constructed with 28 representative plant mitochondrial genomes using the coding sequences of 22 genes under the GTR+G+I model [66]. Mitochondrial-like tRNA genes and protein-coding genes eliminated during evolution are shown in (A) by arrowed black boxes in the evolutionary clades. Genes exceptionally maintained in the branches are shown by arrowed red boxes. (B) shows the chloroplast-derived tRNA genes transferred to the mitochondrial genome as boxes arrowed to a clade, and the genes lost in a branch are shown with an arrow to a box. trnC (GCA) represent tRNA genes of unknown origin, here attributed to chloroplast genes.