Figure 1.
16S rRNA gene tree of AMD Thermoplasmatales Archaea.
Bootstrapping values are indicated as percentages out of 1000 random samples.
Table 1.
Genome information for AMD Thermoplasmatales Archaea.
Figure 2.
Synteny (gene order conservation) versus sequence divergence (average normalized bit score) in pairwise comparisons of 638 Bacterial and Archaeal genomes.
The phylogenetic pairwise comparison method was used to carry out 319 comparisons. See Text S1 for details.
Figure 3.
Synteny (gene order conservation) versus sequence divergence (average normalized bit score) in pairwise comparisons of 638 Bacterial and Archaeal genomes.
Orthologs that are sometimes in predicted operons (operon genes) are compared separately from those that are never in operons (non-operon genes). The circled outliers come from comparisons of endosymbiont genomes, which have very small genomes and greater than expected conserved gene order in non-operon genes.
Figure 4.
Pchance versus percent of syntenous genes that are related.
Pchance is estimated from average normalized bit score, based on the model of GOC versus average normalized bit score. The percentage of syntenous genes that are related is based on data from the STRING protein database.
Table 2.
AIC comparison of regression models for NCBI and STRING data.
Figure 5.
Arrow lengths are proportional to gene lengths. However, intergenic distances are not shown to scale. The colors indicate syntenous genes that we annotated with our synteny-based method. Genes of the same color are in the same syntenous block. Text in blue indicates de novo cobalamin synthesis genes. Text in red indicates cobalamin salvage pathway genes. A) Cobalamin salvage pathway genes. B) De novo cobalamin synthesis pathway genes.
Figure 6.
Molybdopterin synthesis clusters.
Arrow lengths are proportional to gene lengths. However, intergenic distances are not shown to scale. * indicates annotations that are putative. ** indicates genes that are found outside of the cluster. Color indicates syntenous genes that we annotated with our synteny-based method and genes of the same color are in the same syntenous block. A) Cluster 1 B) Cluster 2 C) Clusters 3 and 4.
Figure 7.
Genes related to ether lipid biosynthesis.
Arrow lengths are proportional to gene lengths. However, intergenic distances are not shown to scale. The colors indicate syntenous genes that we annotated with our synteny-based method. Genes of the same color are in the same syntenous block. A) Mevalonate pathway genes B) Ether lipid biosynthesis pathway genes.
Figure 8.
Arrow lengths are proportional to gene lengths. However, intergenic distances are not shown to scale. * indicates annotations that are putative. ** indicates a locus that is unbinned and potentially belongs in the A-plasma genome. The colors indicate syntenous genes that we annotated with our synteny-based method. Genes of the same color are in the same syntenous block.