Table 2.
Identity and probable function of genes showing highest observed values of three statistics (θw, Tajima’s D, and Fu & Li’s D*) in the genome-wide analysis of RSSC phylotypes
| Phylotype/replicon | Gene IDa | Gene name | Number of significant hitsb | Summary statisticsc | Gene description/function | ||
|---|---|---|---|---|---|---|---|
| θw | Tajima’s D | Fu & Li’s D* | |||||
| I/chromosome | RSc2735 | phcB | 5 | 0.0661** | 1.6873** | 1.7108** | Class I SAM-dependent methyltransferase |
| I/chromosome | RSc2736 | phcS | 2 | 0.0729** | 1.6139** | 1.7266** | Two-component sensor histidine kinase |
| I/chromosome | RSc0688 | – | 1 | 0.0482** | 2.9588** | 1.6747** | Glycosyl transferase |
| I/chromosome | RSc2066 | – | 4 | 0.0595** | 3.4633** | 1.7026** | Haloacid dehalogenase-like hydrolase |
| I/chromosome | RSc2670 | lrgB | 1 | 0.0154** | 2.2028** | 1.4372** | Effector of murein hydrolase transmembrane protein |
| I/chromosome | RSc2669 | lrgA | 1 | 0.0210** | 2.4378** | 1.1771* | Effector of murein hydrolase |
| I/megaplasmid | RSp0832 | uxuL | 1 | 0.0155** | 1.6730** | 1.4372** | Glucuronolactone/galactarolactone lactonase |
| I/megaplasmid | RSp0304 | ripD | 2 | 0.0352** | 1.5729** | 1.4062** | Type III effector protein, avrPphD family |
| I/megaplasmid | RSp0487 | ripA4 | 1 | 0.0183** | 2.5310** | 1.4823** | Type III effector protein (formerly AWR4) |
| I/megaplasmid | RSp1212 | ripU | 2 | 0.1156** | 1.4848** | 1.4752** | Type III effector protein |
| I/megaplasmid | RSp0238 | glgX | 1 | 0.0296** | 2.3832** | 1.3369** | Probable pulA pullulanase related glycosidase protein, glycogen debranching enzyme |
| I/megaplasmid | RSp1530 | – | 1 | 0.0944** | 1.5829** | 1.6620** | Polyphenol oxidase (laccase) oxidoreductase |
| I/megaplasmid | RSp1100 | – | 1 | 0.0493** | 2.1856** | 1.3555** | Putative signal sensing transmembrane protein, phosphorelay sensor kinase activity |
| IIA/chromosome | RCFBP_11371 | paaH2 | 1 | 0.0298** | 2.0233** | 1.5364** | Putative 3-hydroxybutyryl-coA dehydrogenase oxidoreductase |
| IIA/chromosome | RCFBP_11349 | – | 1 | 0.0364** | 2.1164** | 1.5632** | Putative high-affinity branched-chain amino acid transport system permease (liv operon) |
| IIA/chromosome | RCFBP_20503 | parC | 1 | 0.0381** | 1.8461** | 1.5686** | DNA topoisomerase IV, subunit A |
| IIA/chromosome | RCFBP_11056 | spec | 1 | 0.0248** | 2.1501** | 1.5085** | Ornithine decarboxylase |
| IIA/chromosome | RCFBP_10967 | ileS | 1 | 0.0248** | 2.0846** | 1.5085** | Isoleucine--tRNA ligase |
| IIA/chromosome | RCFBP_21311 | argC | 1 | 0.0232** | 1.9107** | 1.4970** | N-acetyl-gamma-glutamyl-phosphate reductase |
| IIA/chromosome | RCFBP_10305 | 1 | 0.0282** | 1.9675** | 1.5280** | Putative transcription regulator protein | |
| IIA/chromosome | RCFBP_10218 | soxF | 1 | 0.0248** | 2.0192** | 1.5085** | Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain precursor |
| IIA/chromosome | RCFBP_11858 | bioA | 1 | 0.0265** | 1.9424** | 1.5188** | Adenosylmethionine--8-amino-7-oxononanoate transaminase, PLP-dependent |
| IIA/chromosome | RCFBP_10092 | – | 1 | 0.0381** | 1.9520** | 1.5686** | Putative transporter, with ABC transmembrane type-1 domain |
| IIA/chromosome | RCFBP_10712 | phcQ | 1 | 0.0282** | 1.9908** | 1.5280** | Response regulator receiver |
| IIA/chromosome | RCFBP_10711 | – | 2 | 0.0450** | 2.0770** | 1.5866** | Putative methyltransferase |
| IIA/chromosome | RCFBP_21242 | – | 1 | 0.0414** | 2.5492** | 1.5782** | Putative isomerase, with PhzC/PhzF domain |
| IIA/chromosome | RCFBP_20936 | srkA | 1 | 0.0298** | 2.0897** | 1.5364** | Stress response kinase A |
| IIA/chromosome | RCFBP_10686 | ripW | 2 | 0.0911** | 2.0865** | 1.5603** | Type III effector protein |
| IIA/chromosome | RCFBP_11806 | ripG4 | 2 | 0.0381** | 2.0578** | 1.5686** | Type III effector protein |
| IIA/chromosome | RCFBP_11870 | ripM | 1 | 0.0298** | 2.1673** | 1.5364** | Type III effector protein |
| IIA/chromosome | RCFBP_20594 | ripS5 | 1 | 0.0265** | 1.9424** | 1.5188** | Type III effector protein |
| IIA/megaplasmid | RCFBP_mp10317 | cyaB | 1 | 0.0939** | 0.9326 | 1.5961** | ABC transporter (cyclolysin-type) |
| IIA/megaplasmid | RCFBP_mp10609 | – | 1 | 0.0776** | 1.4690* | 1.1125 | Putative adhesin/hemolysin |
| IIA/megaplasmid | RCFBP_mp30035 | cls | 1 | 0.2490** | 1.7362** | 1.6971** | Cardiolipin synthase A |
| IIA/megaplasmid | RCFBP_mp30119 | – | 1 | 0.0653** | 1.2030* | 1.4386** | Putative type IV fimbrial biogenesis protein pilY1 with A-like domain |
| IIA/megaplasmid | RCFBP_mp30438 | ripF1 | 1 | 0.1** | 1.0458 | 1.5313** | Type III effector protein (formerly PopF1) |
| IIA/megaplasmid | RCFBP_mp20003 | – | 1 | 0.0551** | 1.6353** | 1.0059 | Bacteriophage-related protein of unknown function |
| IIB/chromosome | RSPO_c00124 | atpH | 1 | 0.0226** | 2.1129** | 1.5336** | ATP synthase, f1 sector subunit delta |
| IIB/chromosome | RSPO_c00113 | livK | 1 | 0.0211** | 2.0978** | 1.5182** | Leucine-specific binding precursor transmembrane protein |
| IIB/chromosome | RSPO_c00179 | gcl | 1 | 0.0240** | 2.1552** | 1.5475** | Tartronate-semialdehyde synthase (glyoxylate carboligase) |
| IIB/chromosome | RSPO_c00415 RSPO_c00416 | – | 1 | 0.0352** | 2.0846** | 1.4063** | b-ketoadipate enol-lactone hydrolase protein and 3-ketoacyl-(acyl-carrier-protein) reductase |
| IIB/chromosome | RSPO_c00497 | secY | 1 | 0.0282** | 1.9898** | 1.5826** | Preprotein translocase (membrane subunit) |
| IIB/chromosome | RSPO_c00765 | phcB | 1 | 0.0240** | 2.1264** | 1.5475** | Regulatory protein |
| IIB/chromosome | RSPO_c02646 | pilX | 1 | 0.0211** | 2.0335** | 1.5182** | Putative type IV pili assembly protein |
| IIB/chromosome | RSPO_c01209 | – | 1 | 0.0282** | 2.7986** | 1.5826** | 1-deoxy-d-xylulose-5-phosphate synthase protein |
| IIB/chromosome | RSPO_c01332 | ripAJ | 2 | 0.0226** | 2.2473** | 1.5336** | Type III effector protein |
| IIB/chromosome | RSPO_c02391 | lldP | 1 | 0.0183** | 1.9736** | 1.4823** | l-lactate permease protein |
| IIB/chromosome | RSPO_c02306 | lepA | 1 | 0.0268** | 2.0272** | 1.5718** | GTP-binding elongation factor |
| IIB/chromosome | RSPO_c01998 | ripG7 | 3 | 0.0804** | 2.0276** | 1.4278** | Type III effector protein (formerly GALA7) |
| IIB/chromosome | RSPO_c01999 | ripG6 | 1 | 0.0268** | 2.6851** | 1.5718** | Type III effector protein (formerly GALA6) |
| IIB/chromosome | RSPO_c01798 | aidB | 1 | 0.0536** | 2.2941** | 1.3902** | Isovaleryl CoA dehydrogenase |
| IIB/chromosome | RSPO_c01795 | fadB | 1 | 0,0338** | 2.0162** | 1.6180** | Fused 3-hydroxybutyryl-CoA epimerase |
| IIB/chromosome | RSPO_c00909 | – | 1 | 0.0620** | 3.0207** | 1.5774** | Lipoprotein |
| IIB/chromosome | RSPO_c01066 | metG1 | 1 | 0.0254** | 2.2792** | 1.5602** | Methionyl-tRNA synthetase |
| IIB/chromosome | RSPO_c01082 | spec | 1 | 0.0338** | 2.5566** | 1.3908** | Biodegradative ornithine decarboxylase protein |
| IIB/chromosome | RSPO_c03170 | – | 1 | 0.0354** | 2.0256** | 1.5602** | Chromate transport protein |
| IIB/chromosome | RSPO_c03029 | – | 1 | 0.0312** | 1.9276** | 1.3562** | Sensory box/GGDEF family protein |
| IIB/megaplasmid | RSPO_m01227 | fabI | 1 | 0.0466** | 2.2681** | 1.6703** | Enoyl-[acyl-carrier-protein] reductase (NADH) |
| IIB/megaplasmid | RSPO_m01150 RSPO_m01151 | pehC | 1 | 0.0409** | 2.3366** | 1.4587** | Gluconolactonase and polygalacturonase proteins |
| IIB/megaplasmid | RSPO_m00202 | ripH2 | 9 | 0.0776** | 2.2152** | 1.7322** | Type III effector protein |
| IIB/megaplasmid | RSPO_m00035 | ripG3 | 1 | 0.0676** | 2.3026** | 1.4768** | Type III effector protein (formerly GALA3) |
| IIB/megaplasmid | RSPO_m01206 | ripAO | 1 | 0.0494** | 2.1286** | 1.6788** | Type III effector protein |
| IIB/megaplasmid | RSPO_m01229 | ripS3 | 3 | 0.0409** | 1.9967** | 1.6505** | Type III effector protein (formerly SKWP3) |
| IIB/megaplasmid | RSPO_m01312 | ripZ | 1 | 0.0747** | 2.9580** | 1.7286** | Type III effector protein |
| IIB/megaplasmid | RSPO_m01371 | ripC1 | 1 | 0.0338** | 2.5836** | 1.3908** | Type III effector protein |
| IIB/megaplasmid | RSPO_m00869 | ripN | 1 | 0.0620** | 2.0883** | 1.5774** | Type III effector protein |
| IIB/megaplasmid | RSPO_m00770 | ripAR | 2 | 0.0380** | 2.2529** | 1.6388** | Type III effector protein |
| IIB/megaplasmid | RSPO_m01600 | ripBH | 3 | 0.0620** | 2.7880** | 1.7082** | Type III effector protein |
| IIB/megaplasmid | RSPO_m01541 | ripF1 | 2 | 0.0366** | 2.1843** | 1.6322** | Type III effector protein (formerly PopF1) |
| IV/chromosome | RPSI07_1784 | – | 2 | 0.0312** | 1.5828** | 1.5828** | Putative ABC-type transporter, periplasmic component |
| IV/chromosome | RPSI07_2871 | tyrS | 2 | 0.0312** | 1.5828** | 1.5828** | Tyrosyl-tRNA synthetase |
| IV/chromosome | RPSI07_1208 | rpoD | 3 | 0.0768** | 1.8719** | 1.8719** | RNA polymerase sigma70 factor |
| IV/chromosome | RPSI07_1185 | galU | 2 | 0.048** | 1.6941** | 1.6941** | Glucose-1-phosphate uridylyltransferase |
| IV/chromosome | RPSI07_0660 | mraY | 1 | 0.384** | 1.6419** | 16419** | Phospho-N-acetylmuramoyl-pentapeptide transferase |
| IV/chromosome | RPSI07_0072 | ripE1_1 | 2 | 0,1056** | 1.6690** | 1.6690** | Type III effector protein |
| IV/chromosome | RPSI07_0735 | ripW | 3 | 0.1056** | 1.9186** | 1.6690** | Type III effector protein |
| IV/megaplasmid | RPSI07_mp0105 | – | 1 | 0.1464** | 1.7880** | 1.7880** | Putative acetyltransferase |
| IV/megaplasmid | RPSI07_mp0022 | clcB | 1 | 0.0624** | 1.6238** | 1.6238** | Chloride channel clcB-like protein |
a Systematic gene identifier according to GMI1000, CFBP2957, Po82 or PSI07 strain nomenclature for phylotype I, IIA, IIB or IV respectively
b Number of significant windows overlapping described gene
c Observed values of statistics for each gene and significance of coalescent simulations using standard neutral model: * p < 0.1 and ** p < 0.05