Fig 1.
The simplified schematic diagram showing the chloroplast genome information and variation maps of Chikusichloa mutica.
From outside to inside, all tracks independently represent: 1) the forward strand coding genes; 2) the reverse strand coding genes; 3) the number and distribution of single nucleotide substitutions (SNPs) (black bar color); 4) the number and distribution of non-repeat insertion-deletions (Indels) (purple bar color); 5) the number and distribution of homopolymer structures (grey bar color); 6) the number and distribution of repeat Indels (green bar color). The different functional groups of chloroplast coding genes are colored at the bottom. The diagram was generated with Circos v0.67 (http://circos.ca/).
Table 1.
Base composition in various regions of the Chikusichloa mutica chloroplast genome.
Table 2.
Comparison of major features of 18 Poaceae chloroplast genomes from Ehrhartoideae and Bambusoideae subfamilies.
Table 3.
Comparison of the number of SSRs of 14 chloroplast genomes from rice tribe.
Fig 2.
The variations of border distances between adjacent genes and four junction regions among 16 grasses’ chloroplast genomes.
Boxes above or below the main line indicate the adjacent border genes, which were represented by the different colored boxes at the bottom. The LSC, SSC and two IR regions were also color coded. The distance is not scaled with sequence length.
Table 4.
The number and distribution of polymorphisms of chloroplast genome between two Chikusichloa species.
Fig 3.
The chloroplast phylogenomic trees were generated from 17 grass species.
Three different methods as Bayesian inference (BI), maximum parsimony (MP) and maximum likelihood (ML) were employed to build the tree. Numbers above the branches were the posterior probabilities for BI and bootstrap values of MP and NL. Branch length is proportional to the number of substitutions, as indicated by the scale bar.