Fig 1.
Phylogeny of Papilionoideae modified from Legume Phylogeny Working Group [1–2].
Fig 2.
Plastid genome map of Desmodium heterocarpon, as representative of tribe Desmodieae.
Genes on outside of outer circle are transcribed in clockwise direction; those on inside of outer circle are transcribed in counterclockwise direction. Colored rectangles indicate functional genes, with categories shown on bottom left. Gray scale in inner circle indicates GC content of plastid genome.
Table 1.
Genomic information for species analyzed from tribe Desmodieae and genus Mucuna.
Fig 3.
Desmodieae-specific inversion of gene cluster trnE-UUC, trnY-GUA, and trnD-GUC, mediated by the 11-bp inverted repeats at inversion break points.
(A) Comparisons of inversion for each tribe and subtribe. Nucleotide sequences were simplified in narrow rectangles; same-colored rectangles indicate similar sequence. The 11-bp repeats (blue bars) coincide with break points of inversion. (B) Aligned repeat motifs located upstream of trnT-GGU (Rt) and upstream of psbM (Rp). Rp sequences were reversely aligned.
Fig 4.
Comparison of junctions in plastid genomes sequenced here.
JLA, junction IRa/LSC; JLB, junction IRb/LSC; JSA, junction IRa/SSC; JSB, junction IRb/SSC.
Fig 5.
Maximum likelihood (ML) analysis of 17 legumes (15 Phaseoloid legumes and two outgroups) based on 67 concatenated protein-coding genes.
This tree shown is the one of 1,000 trees derived from ML analysis of 67 concatenated protein-coding gene sequences, log likelihood number = -146379.564971. All nodes were supported with absolute 100% bootstrap values. The fruits of the subtribes [Desmodiinae (multiple-seeded loments) and Lespedezinae (single-seeded legume)] are shown on the side. Asterisks, taxa sequenced here; red and green rectangles on bar, intron and gene losses, respectively, from plastid genome; black rectangles, genome rearrangement events; D, DESMODIUM group; L, LESPEDEZA group; P, PHYLLODIUM group; IRLC, inverted repeat-lacking clade.