Fig 1.
Simplified schematic phylogeny of Papilionoideae, originally published as Figure 1 in Cardoso et al. [4].
Phylogenetic positions are shown for new Sophoreae (incl. Euchresteae and Thermopsideae). *; evolutionary group that includes some former members of Sophoreae s.l. (sensu Polhill [6–7]).
Table 1.
Comparison of features from legume plastomes selected for this study.
Table 2.
Taxa sampled to screen for inversions.
Table 3.
PCR primers used for screening of inversion events.
Fig 2.
Map of Maackia fauriei plastome.
Genes on outside of outer circle are transcribed in clockwise direction; those on inside of outer circle are transcribed in counterclockwise direction. Functional categories of genes are color-coded. Dashed area in inner circle indicates GC content of plastid genome.
Fig 3.
Sequence alignment of intact genes and putative pseudogenes of rps16.
A, intact rps16 in papilionoids; B, putative pseudogene rps16 in genistoids, with comparison to Glycine max (L.) Merr. Frameshift-inducing indels are shaded in red.
Fig 4.
Plastome alignment of LSC regions from Maackia fauriei and other legume species.
Fig 5.
Phylogenetic distribution of 36-kb and 24-kb inversion events in plastomes, as surveyed in our study.
All taxa and their classifications are detailed in Table 2. Arrangement of taxa is based on current understanding about phylogenies of these taxa [3–4, 14–16, 25, 47].
Fig 6.
Maximum likelihood phylogeny tree of legume species inferred by RAxML Blackbox.
Phylogenetic relationships among taxa were generated from concatenated matrix of 71 protein-coding genes with combined aligned length of 53,307 characters. Values at nodes are shown when bootstrap support values are not 100%. Asterisks mark taxa that are not monophyletic.