Fig 1.
Gene map of the complete plastid genome of Iris orchioides.
The conserved plastid genes are presented in the colored boxes. Genes located inward from the black-lined circle are transcribed clockwise, whereas the ones outside the circle are transcribed counter-clockwise. The gray bars shown in the inner circle indicate the GC content.
Table 1.
Summary of the plastid genome characteristics and sample sources of the 20 Iris taxa used in this study.
Collection- and assembly-related information is only presented for the newly sequenced Iris orchioides plastome.
Table 2.
List of genes found in the Iris orchioides plastome.
×2 indicates the genes that were duplicated in the IR regions. Asterisks refer to genes with one (*), two (**), or three introns (***).
Fig 2.
mVISTA plot of the 20 Iris taxa.
The bar indicates the percent sequence identity of the 20 Iris species. I. gatesii was used as a reference sequence to estimate the percent sequence identities.
Fig 3.
Nucleotide diversity (π) plot.
The nucleotide diversity among 20 Iris taxa was estimated. The dashed lines are the borders of the LSC, SSC, and IR regions.
Fig 4.
Comparison of the LSC, SSC, and IR region boundaries among the plastid genomes of 20 Iris taxa.
Table 3.
Summary of simple sequence repeats (SSRs) across varying unit sizes in 20 Iris taxa.
c denotes compound SSRs comprising more than two adjacent SSRs.
Fig 5.
Phylogenetic relationships among 84 accessions of Iris inferred using maximum likelihood (ML) methods based on whole-plastid genomes.
The values presented on each node indicate the bootstrap support.
Fig 6.
Phylogenetic informativeness profiles of 79 coding sequences of Iris estimated in PhyDesign.
The five most informative regions are marked in color.
Fig 7.
Phylogenetic relationships among 84 Iris accessions, inferred using maximum likelihood (ML) methods based on the whole plastome (left) and the best diagnostic marker, the concatenated data with the three high PI genes (rpoC2, ycf1, ycf2) (right).
Dashed lines connect the same samples in both data set. Colors in the trees indicate a subgenus to which the clade belong. Blue- subg. Iris, Red-subg. Limniris, Purple- subg. Scorpiris, Green- subg. Hermodactyloides, Yellow- subg. Xiphium.