Figure 1.
Phylogenetic relationships among STB03, BTS02, and 30 Echinochloa accessions based on the nucleotide sequences of trnT-L-F region of the chloroplast genome.
See the study by Yamaguchi et al. (2005) for code numbers of the 30 accessions [12]. The tree was constructed using NJ method. Bootstrap values with less than 50 are not shown.
Figure 2.
The E. oryzicola chloroplast genome structure and annotation.
Outer circle: The genes shown outside of the circle are transcribed clockwise, whereas those inside are transcribed counterclockwise; Inner circle: the genomic structure with two inverted repeats (IR) and two single copy regions (LSC and SSC). Genes belonging to different functional groups are color coded.
Figure 3.
Visualization of alignments of chloroplast genome sequences.
The sequence identity was plotted with the E.oryzicola chloroplast genome as the reference. Sequence identity with 50%–100% is shown. Exonic regions and conserved non-coding sequences (CNS) are colored in blue and red, respectively.
Figure 4.
Divergence time of the genus Echinochloa.
Divergence time was estimated using BEAST based on the complete chloroplast genomes of six species (E. oryzicola, E. crus-galli, P. virgatum, S. bicolor, Z. mays, and O. sativa). The numbers showed at nodes indicate divergence time.