Fig 1.
Circular map of the plastid genome of the cryptophyte Teleaulax amphioxeia.
All of the genes are transcribed in a clockwise direction. Note the dense gene arrangement and the single large intergenic region. The protein-coding genes and ribosomal RNA and transfer RNA genes are labeled inside or outside of the circle. The genes are color coded according to the functional categories listed in the index below the map.
Table 1.
Characteristics of the cryptophyte plastid genome analyzed in this study.
Table 2.
tRNA sequences present in the cryptophyte plastid genome.
Table 3.
List of genes in the Teleaulax amphioxeia plastid genome (143 total).
Fig 2.
Overview of the red algal plastid genomes.
Linearized maps of the complete T. amphioxeia plastid genome is compared with those of other cryptophytes. Color-coded syntenic blocks are shown above each genome, and gene maps are shown below each genome. The syntenic blocks above the horizontal line are on the same strand, and those below the line are on the opposite strand. The horizontal bars inside of the syntenic blocks indicate sequence conservation. The block boundaries correspond to sites at which inversion events occurred. On the gene maps, the genes above the horizontal line are transcribed from left to right, and those below the horizontal line are transcribed from right to left. The rRNA operons are shown in red.
Fig 3.
Phylogenetic tree of the cryptophyte plastids.
(A) RAxML phylogeny constructed from a concatenate of 93 proteins (18,180 amino acids). The ML and MP bootstrap values are shown above or below the branches. (B) A simple overview of cryptophyte plastid gene synteny. (C) RAxML phylogeny constructed based on 93 protein-coding genes (56,569 nucleotides). The ML, MP and NJ bootstrap values are shown above or below the branches. The bold branches indicate strongly supported values (ML, MP, and NJ = 100%). The asterisks indicate supported values = 100%, and the dashes indicate values with < 50% support. The scale bar depicts the number of substitutions/site.