Fig 1.
Close-up microscope photo of Spanish moss (Tillandsia usneoides L.).
Peltate scales (trichomes) are displayed.
Fig 2.
Phylogenetic tree showing the major clades and families of Poales, simplified from APG IV [16].
Dashed lines indicate families with uncertain position. Numbers indicate the available plastid genome sequences in NCBI Organelle Genome Resources (searched on 8.11.2016). Asterisk in case of Cyperaceae indicate the presence of one available (Carex siderosticta, NC027250) but currently unpublished sequence.
Fig 3.
The circular representation of the plastid genome of Spanish moss (Tillandisa usneoides).
Structural organization of the gene content ring was color coded based on its functional category. The innermost circle denotes the GC content across the genome. The genes that were transcribed counter-clockwise and clockwise were at the outer and inner ring, respectively. The illustration was drawn using OGDRAW.
Table 1.
List of genes in the chloroplast genome of Spanish moss.
Table 2.
The genes having intron in the Tillandsia usneoides plastid genome and the length of the exons and introns.
Table 3.
Relative synonymous codon usage (RSCU) of Tillandsia usneoides is given in parentheses following the codon frequency.
Table 4.
Repeat sequences of Tillandsia usenoides chloroplast genome.
Table 5.
Estimates of average evolutionary divergence over 80 protein coding-gene sequences from Poales.
Standard error estimate(s) are shown in the fourth column and were obtained by a bootstrap procedure (1000 replicates). The ten most divergent genes are shown in part A, while the ten most conserved genes are listed in part B.
Table 6.
Comparison of major features of Tillandsia usneoides and nine commelinid plastid genomes.
Fig 4.
Multipip analysis showing overall sequence similarity of plastid genomes based on complete genome alignment.
Levels of sequence similarity are indicated by red (75–100%), green (50–75%) and white (<50%). Comparison was made for ten plastid genomes using Tillandsia usneoides as the reference genome. Arrows indicate gene/intron losses and deletions; partial duplication of the ycf1 is due to IR expansion.
Fig 5.
A. Tillandsia usneoides compared to Triticum aestivum, showing the three major inversions specific for grasses. B. Ananas comosus compared to T. usneoides.
Fig 6.
Comparison of plastid borders of LSC, SSC and IR regions among selected species of Poales.
Selected genes or portions of genes are indicated by colored boxes. Gene and region lengths are not to scale (see Table 6).
Fig 7.
Maximum likelihood (ML) tree of 80 protein coding genes of Poales.
Tree of the parsimony analysis was congruent with the ML tree displayed. Topological differences are indicated by dashed lines restricted to the sister grouping of Typhaceae resolved only with parsimony. Bootstrap values less than 100 are shown at nodes for parsimony/ML. Genomic changes are indicated by black bars.