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Table 4 Genes under positive selection.

From: Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes

Gene locus Gene description (gene symbol) COG(1) Recombination(2) Branch under pos. selection Q-value ω(3) p(4) BEB (P> 95%)(5)
Lmo0098 PTS system, mannose/fructose/sorbose family, IID component (mptD) NCOG GCV; MAX LI/LM 0.170 472.58 0.004 -
Lmo0099 conserved hypothetical protein NCOG - LI/LM 0.170 0.009 -
Lmo0139 conserved hypothetical protein NCOG - LM2A 0.160 56.74 0.054 95
Lmo0297 PRD/PTS system IIA 2 domain protein K; G; T GCV; MAX; NSS; PHI LM2A 0.164 0.012 499
Lmo0397 conserved hypothetical protein S GCV; MAX LM2A 0.1264 0.043 -
Lmo0429 glycosyl hydrolase, family 38 G GCV; MAX; NSS; PHI LM2A 0.0325 977.51 0.008 667
Lmo0455 conserved hypothetical protein T; Q GCV; MAX; NSS; PHI LM2A 0.1214 0.004 -
Lmo0653 conserved hypothetical protein S MAX LM2A 0.033 0.012 306
Lmo0658 endonuclease III domain protein L MAX; NSS LM2A 0.108 0.023 209
Lmo0692 chemotaxis protein CheA (cheA) T; N GCV; MAX; NSS; PHI LM1A 0.156 0.002 -
Lmo0693 flagellar motor switch domain protein N; U - LM2A 0.007 0.022 -
Lmo0695 conserved hypothetical protein NCOG MAX; NSS; PHI LM1A 0.175 0.014 -
Lmo0732 cell wall surface anchor family protein NCOG GCV LM1A 0.185 6.92 0.076 -
Lmo0782 PTS system, mannose/fructose/sorbose family, IIC component (mpoD) NCOG GCV; MAX Overall; 0.146; 88.23; 0.008; -
     LM1A; 0.052; ∞; 0.0001; -
     LM2A 0.098 0.004 -
Lmo0785 sigma-54 dependent Kal regulator (manR) K; T GCV; MAX LM2A 0.129 1.00 0.000 -
Lmo0872 major facilitator family transporter G GCV; MAX; NSS LM2A 0.137 0.008 -
Lmo0910 putative membrane protein R MAX; NSS LM1A 0.019 0.012 -
Lmo1146 conserved hypothetical protein NCOG GCV; MAX LI/LM 0.046 223.37 0.023 169
Lmo1164 PduO protein (pduO) S; R GCV LI/LM 0.170 195.87 0.038 -
Lmo1412 DNA topology modulation protein FlaR (flaR) F - LM2A 0.160 8.56 0.139 12; 37; 68
Lmo1424 transporter, NRAMP family (mntH) P GCV LM1A 0.185 1.00 0.000 -
Lmo1523 GTP pyrophosphokinase (relA) K; T - LM2A 0.033 1.00 0.000 -
Lmo1529 preprotein translocase, YajC subunit U - LI/LM 0.170 0.011 -
Lmo2102 glutamine amidotransferase, SNO family (pdxT) H GCV; MAX; NSS; PHI LM1A 0.185 0.017 66
Lmo2121 glycosyl transferase, family 65 G GCV; MAX; NSS LM1A 7.6E-06 35.31 0.031 722; 723; 725; 729; 730; 744; 752;
Lmo2178 cell wall surface anchor family protein M GCV; MAX; NSS; PHI LI/LM; 0.193; 15.92; 0.001; -
     LM2A 0.137 5.34 0.025 1769
Lmo2215 ABC transporter, ATP-binding protein V MAX; NSS Overall 0.188 14.23 0.008 -
Lmo2222 Ser/Thr protein phosphatase family protein L GCV; MAX LM2A 0.160 0.021 253
Lmo2446 glycosyl hydrolase, family 31 G GCV; MAX; NSS; PHI LM2A 0.003 0.0001 -
Lmo2596 ribosomal protein S9 (rpsI) NCOG - LM2A 0.021 0.010 -
Lmo2611 adenylate kinase (adk) F GCV; MAX LM2A 0.120 24.80 0.013 -
Lmo2724 conserved hypothetical protein S NSS LI/LM 0.170 0.008 -
Lmo2802 glucose-inhibited division protein B (girB) M GCV; MAX; NSS; PHI LM1A 0.046 0.013 -
Lmo2804 conserved hypothetical protein NCOG GCV; MAX; NSS; PHI Overall 6.5E-17 16.53 0.044 -
Lmo2824 D-isomer specific 2- hydroxyacid dehydrogenase family protein E; H GCV; MAX; NSS LM2A 0.160 229.62 0.003 -
  1. (1) NCOG: Not in COGs; K: Transcription; G: Carbohydrate transport and metabolism; T: Signal transduction mechanisms; S: Function unknown; Q: Secondary metabolites biosynthesis, transport and catabolism; L: Replication, recombination and repair; N: Cell motility; U: Intracellular trafficking and secretion; R: General function prediction only; F: Nucleotide transport and metabolism; P: Inorganic ion transport and metabolism; E: Amino acid transport and metabolism; H: Coenzyme transport and metabolism; M: Cell wall/membrane biogenesis; V: Defense mechanisms
  2. (2) GCV: GENECONV; MAX: Maximum χ2; NSS: Neighbour Similarity Score; PHI: Pairwise Homoplasy Test
  3. (3) ω = dN/dS (Number of nonsynonymous changes per nonsynonymous sites/Number of synonymous changes per synonymous sites); infinite values of ω (∞) indicate that the model did not find synonymous changes for the branches tested (dS = 0; ω ~ ∞). However, this (i.e., ω ~ ∞) does not affect the validity of the Likelihood Ratio Test, which was used to identify the genes under positive selection (Z. Yang, pers. Communication; see http://gsf.gc.ucdavis.edu/viewtopic.php?f=1&t=2079&sid=c4a82e1ca334ca84a00a8b85e0f33c9d and http://gsf.gc.ucdavis.edu/viewtopic.php?f=1&t=2329&sid=c4a82e1ca334ca84a00a8b85e0f33c9d;
  4. (4) Proportion of sites under positive selection
  5. (5) This column lists sites identified using Bayes Empirical Bayes (BEB) as being under positive selection; numbers identify the amino acid sites (in alignments) that are under positive selection