Genome sequencing of the yellow-pigmented, thermophilic bacterium Thermus sp. NMX2.A1
resulted in a 2.29 Mb draft genome that encodes for 2312 proteins. The genetic relationship between
various strains from the genus Thermus was assessed based on phylogenomic analyses using a concatenated
set of conserved proteins. The resulting phylogenetic tree illustrated that Thermus sp. NMX2 A.1
clusters together with Thermus scotoductus SA-01, despite being isolated from vastly different geographical
locations. The close evolutionary relationship and metabolic parallels between the two strains has
previously been recognized; however, neither strain’s genome data were available at that point in time.
Genomic comparison of the Thermus sp. NMX2.A1 and T. scotoductus SA-01, as well as other closely
related Thermus strains, revealed a high degree of synteny at both the genomic and proteomic level, with
processes such as denitrification and natural cell competence appearing to be conserved. However, despite
this high level of similarity, analysis revealed a complete, putative Calvin–Benson–Bassham (CBB) cycle in
NMX2.A1 that is absent in SA-01. Analysis of horizontally transferred gene islands provide evidence that
NMX2 selected these genes due to pressure from its HCO3
- rich environment, which is in stark contrast to
that of the deep subsurface isolated SA-01.