Skip to main content

Table 3 Serotype-associated core genes undergoing positive selection specifically on AMR S. Dublin, S. Newport or S. Typhimurium ancestral branches

From: Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica

Gene Ln L MA1a Ln L MAb p valuec FDRd Functione ωf proportion of sites under pos. Selection(%)g
S. Dublin branch
 Cluster_1190 − 7073.691 − 7048.222 0.000 0.000 autotransporter outer membrane beta-barrel domain-containing protein 569.327 5.984
 Cluster_1721 − 1052.362 − 1038.860 0.000 0.000 dipeptidase E 999.000 1.364
 Cluster_1900 −2015.241 −2004.734 0.000 0.002 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase 999.000 0.526
 Cluster_2035 − 2457.111 − 2446.938 0.000 0.002 flagellar M-ring protein FliF 999.000 0.482
 Cluster_3324 −778.864 − 771.694 0.000 0.032 fimbrial protein StiA 999.000 0.804
S. Newport branch
 Cluster_831 − 1041.959 − 1024.731 0.000 0.000 ABC transporter ATP-binding protein 999.000 3.724
 Cluster_875 −844.370 − 826.859 0.000 0.000 CaiF/GrlA family transcriptional regulator 999.000 4.986
 Cluster_1190 − 7071.499 − 7051.968 0.000 0.000 autotransporter outer membrane beta-barrel domain-containing protein 999.000 6.661
 Cluster_1461 − 4112.903 − 4103.963 0.000 0.003 2-oxoglutarate dehydrogenase E1 component 999.000 0.113
 Cluster_1538 − 2076.594 − 2066.164 0.000 0.001 invasin 999.000 0.295
 Cluster_1678 −2008.961 −2001.754 0.000 0.019 hypothetical protein 204.362 0.829
 Cluster_3346 − 1744.612 − 1726.105 0.000 0.000 hypothetical protein 999.000 11.655
 Cluster_3368 − 4010.845 − 3976.156 0.000 0.000 outer membrane protein assembly factor BamA 836.419 3.378
S. Typhimurium branch
 Cluster_476 −1969.539 − 1933.139 0.000 0.000 porin 859.863 7.172
 Cluster_1190 − 7076.553 −7037.396 0.000 0.000 autotransporter outer membrane beta-barrel domain-containing protein 252.954 7.072
 Cluster_1216 − 2790.059 − 2781.805 0.000 0.008 maltodextrin glucosidase 999.000 0.764
 Cluster_1756 − 2830.518 − 2823.397 0.000 0.024 glutamine--fructose-6-phosphate aminotransferase 828.247 0.394
 Cluster_2234 −1998.702 −1990.410 0.000 0.008 tryptophan permease 999.000 1.035
 Cluster_2311 − 3370.510 − 3358.161 0.000 0.000 E3 ubiquitin--protein ligase 171.701 1.404
 Cluster_2757 − 2077.394 − 2068.717 0.000 0.008 D-serine/D-alanine/glycine transporter 106.317 1.691
  1. aLn L MA1; Lognormal likelihood score for the null hypothesis that sites evolved following neutral model in the serotype ancestral branch
  2. bLn L MA; Lognormal likelihood score for the alternative hypothesis that sites evolved under positive selection in the serotype ancestral branch
  3. cThe test statistic was calculated as 2[(−Ln L MA1) - (−Ln L MA)]
  4. dThis column indicates the p-value after a FDR (False Discovery Rate) correction was carried out to correct for multiple comparison
  5. e“Function” represents the gene function provided by the NCBI Prokaryotic Genome Annotation Pipeline
  6. fω, average dN/dS value for codon sites under positive selection. dN is the number of nonsynonymous changes divided by the number of nonsynonymous sites. dS is the number of synonymous changes divided by the number of synonymous sites. ω = 999.000 represent infinite values as dS = 0
  7. gproportion of codon sites under positive selection