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Table 2 Orthologous genes with evidence of homologous recombination detected by both PHI and RDP4

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

Gene No. of taxaa Functionb Serotype-associatedc PHI p value RDPd GENECONVd Bootscand Maxchid Chimaerad SiSscand 3Seqd
Cluster_25 90 oxidoreductase FeS-binding subunit N 0.004813     3.74E-03 2.87E-02 4.17E-08 0.03547
Cluster_32 90 MFS transporter N < 0.0005 2.75E-05   3.02E-02 6.11E-10   2.20E-22 3.23E-07
Cluster_52 64 phage tail protein N < 0.0005 7.38E-17 5.85E-18 3.99E-18 6.09E-12 9.23E-13 3.88E-15 2.81E-24
Cluster_3844 64 phage tail protein N < 0.0005 9.42E-10 3.59E-07 2.92E-06 1.13E-11 3.03E-13 1.04E-15 7.99E-18
Cluster_3925 70 phage tail protein N 0.004785 2.93E-03    5.82E-10 3.01E-07 3.85E-23 7.85E-05
Cluster_4291 57 phage tail protein I Y < 0.0005    3.10E-03 2.07E-07 3.77E-05   3.30E-05
Cluster_4292 57 recombinase Y 0.01689 4.56E-03 8.03E-03 4.72E-03 6.89E-06 1.32E-06 1.01E-04 2.34E-06
Cluster_4306 52 mercuric transport protein periplasmic component N 0.007786   1.51E-08   6.83E-05 8.67E-04   3.06E-03
Cluster_4307 52 mercuric transport protein N 0.002263 3.91E-07 7.08E-06 2.05E-07 5.77E-05 2.23E-04 1.57E-09 1.01E-06
Cluster_4308 53 portal protein Y < 0.0005 2.37E-14 9.40E-09 2.38E-14 3.37E-14    2.66E-27
Cluster_4309 53 hypothetical protein Y < 0.0005 1.72E-05 2.65E-03   1.63E-12 9.43E-08   4.90E-06
Cluster_4310 53 DNA transfer protein Y 0.002031 1.30E-03 7.12E-04   6.10E-08 2.54E-04 4.43E-05 1.73E-04
Cluster_4343 53 RecBCD nuclease inhibitor Y < 0.0005 3.10E-05 2.10E-05 3.09E-06 4.82E-08 2.58E-06 1.16E-08 1.51E-06
Cluster_4344 53 recombinase Y < 0.0005   1.05E-02   3.44E-02 2.66E-02   2.01E-04
Cluster_4345 53 hypothetical protein Y < 0.0005   5.39E-04 5.88E-04 3.18E-07 2.55E-03 2.45E-09 4.45E-03
Cluster_4355 52 phage tail protein Y < 0.0005 1.13E-09 7.64E-04 2.42E-06 3.57E-11 1.02E-03   3.51E-02
Cluster_4361 48 peptidase Y < 0.0005 3.81E-09   3.92E-12 4.40E-04 3.19E-05   1.13E-07
Cluster_4432 48 terminase Y < 0.0005 2.89E-11 3.68E-10 2.02E-09 1.67E-17 7.22E-08 1.55E-42 4.83E-46
Cluster_4484 49 endonuclease Y < 0.0005 1.81E-17 2.25E-18 3.38E-14 2.63E-03 1.42E-03 8.97E-35 1.08E-36
Cluster_4488 40 phage tail tape measure protein Y < 0.0005 2.99E-02 3.41E-03 1.81E-04 1.26E-04 6.51E-03 2.38E-17 1.73E-12
Cluster_4533 47 phage portal protein Y < 0.0005 2.78E-10 6.75E-10 5.49E-09 5.22E-10 7.45E-04 9.57E-18 9.99E-18
Cluster_4534 47 capsid protein Y 0.01974     9.04E-09 3.53E-03 4.91E-09 2.78E-03
Cluster_4543 47 baseplate assembly protein Y < 0.0005 2.80E-07 6.92E-18 4.96E-03 3.08E-19 5.29E-09 5.49E-03 1.26E-23
Cluster_4548 47 phage tail tape measure protein Y 0.01543     3.98E-03 3.09E-03 4.16E-04 1.25E-02
Cluster_4549 47 phage tail protein Y 0.008323 3.81E-84 3.34E-76 4.42E-76 9.86E-40 1.45E-41 6.19E-30 4.44E-16
Cluster_4562 46 acyltransferase Y < 0.0005   1.26E-06 3.40E-09 8.88E-09 4.05E-05 1.26E-11 4.13E-06
Cluster_4594 44 coat protein Y < 0.0005   8.20E-94 2.62E-96 2.28E-24 1.67E-24 3.81E-31 2.22E-15
Cluster_4595 44 endorhamnosidase Y < 0.0005 5.09E-12 2.93E-10 6.52E-12 4.87E-11 4.76E-12 5.27E-11 7.77E-15
Cluster_4658 31 hypothetical protein Y < 0.0005 2.26E-06 2.30E-03   5.76E-04 1.95E-03   9.80E-04
Cluster_4805 37 DNA-invertase N < 0.0005 2.98E-41 3.16E-35 5.25E-38 8.71E-15 2.73E-11 1.33E-12 8.88E-16
Cluster_4879 31 DNA transfer protein Y 0.001663 8.93E-11 2.59E-05 2.43E-06 2.58E-13 2.32E-02 2.16E-09 1.82E-04
Cluster_5031 31 protein NinG Y < 0.0005 2.85E-08 3.32E-09   8.24E-08 4.16E-08 1.95E-10 1.21E-09
Cluster_5479 19 resolvase Y < 0.0005 3.90E-09 8.64E-07 4.57E-08 5.37E-10 9.25E-09 9.55E-07 6.43E-13
Cluster_5556 17 replication of DNA Y < 0.0005   6.88E-30 1.04E-43 9.83E-28   4.13E-29 7.14E-79
Cluster_5572 16 DNA methylase Y < 0.0005 4.00E-03 1.32E-03   9.25E-04 7.54E-05 3.24E-05 1.52E-03
Cluster_5598 15 methyltransferase Y 0.00691 1.70E-02   5.20E-03 2.55E-05    6.62E-05
Cluster_5601 15 relaxase NikB Y < 0.0005 1.36E-08 3.65E-05 1.39E-08 9.80E-10    2.41E-15
Cluster_5602 15 conjugal transfer protein TrbC Y 0.02477    6.49E-03 3.23E-04 4.18E-03   2.77E-02
Cluster_5607 15 hypothetical protein Y < 0.0005 3.06E-19 8.34E-20 3.60E-21 1.58E-17 2.82E-19 7.02E-17 1.11E-15
Cluster_5609 15 conjugal transfer protein Y < 0.0005   1.98E-02 6.21E-04 2.37E-04    1.92E-05
Cluster_5640 15 hypothetical protein Y 0.005552 3.33E-02 5.88E-03 3.31E-04 1.36E-02 6.51E-03 1.18E-04 5.09E-04
Cluster_6042 5 oxaloacetate decarboxylase N < 0.0005   6.88E-03 2.66E-02 9.52E-05    1.27E-07
  1. aNumber of isolates with the corresponding cluster gene
  2. bFunction was determined by NCBI Prokaryotic Genome Annotation Pipeline
  3. cY: serotype-clustered core genes (i.e., showed clustering by serotype in the gene tree), or serotype-associated accessory genes (i.e., significantly over- or under- represented in one serotype)
  4. N not serotype-clustered core genes nor serotype-associated accessory genes
  5. dp value of the statistic test; only significant p-values (< 0.05) are shown