Skip to main content
. 2020 Jul 21;11(4):e00766-20. doi: 10.1128/mBio.00766-20

FIG 4.

FIG 4

Neighbor-joining distance trees of different gene sets encoding HEP, LEP, and their associated conserved (cr) and variable (vr) regions based on the corresponding modal codon usage. Modal codon usage-based neighbor-joining trees with black branches were constructed for the indicated natural gene sets and their intragenic regions (cr and vr) following the method described by Karberg et al. (17) along with the neighbor-joining program of the Phylip package (62). Artificially simulated sequences were used as controls in the neighbor-joining tree (SIM labeled data and gray branches in the tree). Such artificially generated sequences were evolved under a model with no pressure for codon selection and preserving the same KA/KS ratio as that corresponding to each of their natural HEP/LEP set of homologs (see Materials and Methods). LEP_cr-SIM sequences are not included since, on average, fewer than 53 conserved amino acid positions/protein were collected in the simulation. Phylogenetic trees were drawn through the use of the Figtree application (59). Abbreviations: C1 to Ci, core gene sets with increasing ancestry; single, singletons; HEP, genes encoding proteins with the highest expression level; LEP, genes encoding proteins with the lowest expression level; HEP_cr, conserved HEP sequences (dark red); HEP_vr, variable HEP sequences (light red); LEP_cr, conserved LEP sequences (dark blue); and LEP_vr, variable LEP sequences (light blue). HEP and LEP cr and vr subfractions were recovered as indicated in Materials and Methods through the use of the polypeptide sequences included in C13 for Yersinia enterocolitica subsp. palearctica Y11, C10 for Streptococcus equi ATCC 33398, C8 for Sulfurospirillum multivorans DSM 12446, C9 for Bacillus subtilis subsp. spizizenii TU B 10, C6 for Bacteroides vulgatus ATCC 8482, and C12 for Mycobacterium fortuitum subsp. fortuitum DSM 46621 (ATCC 6841). The effective number of codons (Ncs) as previously defined by Wright (71) are indicated in parentheses for the cr and vr subset of sequences.