Fig 1.
Genomic map of the Utricularia reniformis cp genome.
Genes shown on the outside of the map are transcribed clockwise, whereas genes on the inside are transcribed counter-clockwise. Genes are color coded by their function in the legend.
Table 1.
List of genes encoded by the Utricularia reniformis chloroplast (cp) genome.
Table 2.
Codon usage and codon—anticodon recognition pattern for tRNA in Utricularia reniformis cp genome.
Fig 2.
Expression profile of the Utricularia reniformis cp genes.
The expression values are normalized in Reads Per Kilobase per Million mapped reads (RPKM) on the Y-axis. The psaJ and psbA genes show the highest expression levels as measured in RPKM (323,750 and 437,421, respectively) and were suppressed from the figure for clarity.
Table 3.
RNA editing pattern in Utricularia reniformis cp genome identified by RNAseq reads alignment.
Table 4.
RNA editing pattern in Utricularia reniformis cp genome predicted by PREP-Cp.
Fig 3.
Frequency of SSR motifs found in Utricularia reniformis cp coding and intergenic regions, taking into account sequence complementarities.
Table 5.
Distribution of the cpSSRs present in the U. reniformis cp coding regions.
Table 6.
Sequence repeats in the cp genome of Utricularia reniformis.
Type, location and size (in bp) of repeated elements (IGS, Intergenic spacer).
Fig 4.
Comparison of the boundaries of the LSC, SSC, and IR regions in the currently available cp genomes of Lentibulariaceae.
Fig 5.
Venn diagram showing the full complement of genes present in the sequenced Lentibulariaceae cp genomes (pan genome).
The tRNAs and rRNAs are not included. The numbers below each species represent the unique genes used in the comparison.
Table 7.
Distribution and comparisons of the eleven genes in the ndh complex, encoded in aquatic and terrestrial cp genomes from carnivorous plants and the ancestral lineages Sesamum indicum, Tanaecium tetragonolobum and Andrographis paniculata.
Black box represents that the given ndh gene is present and intact. Gray box indicates truncated ndh gene according to the legend. White box indicate that the given ndh gene is absent in the cp genome.
Fig 6.
Phylogenetic history of ndh genes.
(A) represents the only scenario for the ndhA, ndhC, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, and ndhK genes evolution. (B) represents the phylogenetic history and the two possible scenarios for the ndhB gene and (C) for the ndhD gene (blue bars indicate the arising of the functional genes and red bars their loss).
Fig 7.
Phylogenomic analysis based on 23 complete Lamiales cp genomes.
The phylogenetic position of Utricularia reniformis was inferred by maximum likelihood and Bayesian analyses. Numbers above and below the lines indicate the maximum likelihood bootstrap values and Bayesian posterior probabilities values > 50% for each clade, respectively. The table on the right indicates the genome features in base pairs (chloroplast genome length, LSC, SSC and IRs regions). The histograms located to the left of each feature (CP size, LSC, SSC and IRs), graphically illustrate the size distribution for each feature. Sub-titles: I Lentibulariaceae; II Acanthaceae; III Bignoniaceae; IV Pedaliaceae; V Orobanchaceae; VI Lamiaceae; VII Scrophulariaceae; VIII Gesneriaceae, and IX Oleaceae.
Fig 8.
Cloudgram (Bayesian inference) of Lentibulariaceae from 18,000 Bayesian trees based on matK cp gene.
The red circle 1 indicates the terrestrial ancestral lineage for the Lentibulariaceae family. The blue circles, 2 and 2’, represent the independent radiations to the aquatic habitat of Utricularia lineages. The green circle 3 indicates the possible ancestor of the epiphytic species from the plesiomorphic terrestrial life form, and the black circles, 4 and 4’, represent the independent origins for the rare reophytic life form for Utricularia lineages. Numbers below clades represent the support (maximum parsimony bootstrap/ maximum likelihood bootstrap/ posterior probabilities based on Bayesian inference). Higher color densities represent higher levels of certainty represented by congruent trees (from the 18,000 trees).