Here, we explicate in detail the bioinformatic analyses we conducted.

In the following, all sequences and genes belonging to Pseudomonas syringae pathovars which have been deposited in GenBank are listed. The figures in parentheses – following the name of pathovars- refer to the number of genes of the relevant pathovar deposited in GenBank. In some cases the sequence of complete genome of pathovar is available. In our analysis in order to choose the hrcVgene and also conduct bioinformatic analyses we used all the sequences which have been listed here. This list is the most encompassing and update catalogue of sequences relating to Pseudomonas syringae pathovars which up to now has been deposited in GenBank. Hence, we tried to perform our bioinformatic analyses taking advantage of as many as available sequences of Pseudomonas syringae pathovars

  • Pseudomonas syringae pv. atropurpurea(4 genes). CmaU (cmaU) gene, cdspartial rpoD, strain NCPPB gene for 16S rRNA,partial rpoB gene for RNA polymerase beta subunit, strain CFBP 234
  • Pseudomonas syringae pv. coronafaciens (17 genes: (cpn60) gene, hrpS, hrpA, hrpZ, hrpB genes, 1- LMG OprF (oprF) gene, 16S-23S ribosomal RNA - KN221 hopZ1 p sequence, strain 3113 hopZ1 ,strain KN221 type III effector HopZ2 (hopZ2) gene, complete cds,KN 221 sigma 70 factor (rpoD) gene, rpoD-1 allele, partial cds,KN 221 glucose-6-phosphate isomerase (pgi) gene, pgi-25 allele, partial cds, KN 221 gyrase B (gyrB) gene, gyrB-29 allele, partial cds,KN 221 citrate synthase I (gltA) gene, gltA-1 allele, partial cds,KN 221 glyceraldehyde-3-phosphate dehydrogenase (gap1) gene, gap1-22 allele, partial cds-- KN 221 aconitase B (acnB) gene, acnB-15 allele, partial,CMP 3113 16S-23S , partial rpoD gene for RNA polymerase sigma factor,
  • Pseudomonas syringae pv. garcae(19 genes): rpoD gene ,pPG2708 B0046 protein gene, partial cds,1634 RpoD (rpoD) gene, partial cds,1634 GyrB (gyrB) gene, partial cds,plasmid p1634B RepA (repA) gene, complete cds,p1634A TraY (traY) gene, partial cds,pPSM9032A TraY (traY) gene, partial cds,plasmid pPG2708 TraY (traY) gene, partial cds,p1634A B0077 protein gene, partial cds,pPG2708 B0077 protein gene, partial cds,2708 RpoD (rpoD) gene, partial cds,2708 GyrB (gyrB) gene, partial cds,p1634A RepA (repA) gene, complete cds,p1634B TraY (traY) gene, TraY (traY) gene ,16S-23S ribosomal RNA intergenic,,16S-23S,rpoB gene
  • Pseudomonas syringae pv. oryzae
  • Pseudomonas syringae pv. oryzae str. 1_6(complete genome)
  • Pseudomonas syringae pv. porri (5 genes): (rpoB)gen, (rpoD) gene, (gyrB) gene, BD 369 16S-23S , l rRNA gene,
  • Pseudomonas syringae pv. striafaciens

Pseudomonas sp. NBRC 3309 (1gene for 16S rRNA, partial sequence)

  • Pseudomonas syringae pv. zizaniae (2 genes(: rpoD gene, partial rpoB gene
  • Pseudomonas syringae group genomosp.
  • Pseudomonas syringae
  • Pseudomonas syringae Cit 7(complete genome)
  • Pseudomonas syringae DM2.1.12.02A(complete genome)
  • Pseudomonas syringae ICMP 18804(complete genome)
  • Pseudomonas syringae ICMP 18806(complete genome)
  • Pseudomonas syringae KN2.a.3(complete genome)
  • Pseudomonas syringae Knox623a( complete genome)
  • Pseudomonas syringae Knox652c( complete genome)
  • Pseudomonas syringae LMC.P10( complete genome)
  • Pseudomonas syringae LMC.P80( complete genome)
  • Pseudomonas syringae LMC.P91( complete genome)
  • Pseudomonas syringae LP205a( complete genome)
  • Pseudomonas syringae LP217a( complete genome)
  • Pseudomonas syringae LP221b( complete genome)
  • Pseudomonas syringae LP868.1a( complete genome)
  • Pseudomonas syringae ME.Cv.P30( complete genome)
  • Pseudomonas syringae ME.Dv.P42( complete genome)
  • Pseudomonas syringae ME812.2b( complete genome)
  • Pseudomonas syringae NL.P1 3(complete genome)
  • Pseudomonas syringae NP29.1a(complete genome)
  • Pseudomonas syringae pv. aceris (complete genome)
  • Pseudomonas syringae pv. aptata(complete genome)
  • Pseudomonas syringae pv. atrofaciens (complete genome)
  • Pseudomonas syringae pv. averrhoi(40 genes): HL1 type III effector HopAT1 (hopAT1), type III effector HopAJ1 (hopAJ1), and hypothetical protein genes, complete cds; and hypothetical protein gene, partial cds-- 3-phosphoshikimate 1-carboxyvinyltransferase (aroA), ChrR, RNA,strain HL1 leucyl-tRNA synthetase (leuS) gene, partial cds; putative lipoprotein, DNA polymerase III delta subunit (holA), HopAJ2 protein (hopAJ2), lipoic acid synthetase (lipA), and B (lipB) genes, cFlgJ (flgJ) gene, partial cds; FlgK (flgK), FlgL (flgL), glycosyltransferases, 3-oxoacyl-(acyl-carrier-protein) synthase III, FliC (fliC), FlaG (flaG), FliD (fliD), FliS (fliS), FliT (fliT), and FleQ (fleQ) genes, complete cds; and FleS (fleS) gene, partial cds)
  • Pseudomonas syringae pv. avii (1 gene ):rpoD gene for RNA polymerase sigma factor, strain NCPPB 4290)
  • Pseudomonas syringae pv. dysoxyli (4 genes) : (tpmE) gene, partial cds, sigma 70 factor (hrpL) gene, rpoD gene for RNA polymerase sigma factor, strain NCPPB 225, partial rpoB gene)
  • Pseudomonas syringae pv. japonica( complete genome)
  • Pseudomonas syringae pv. lapsa ( 11 genes) : (tpmE) gene, partial cds,hrpS, hrpA, hrpZ, hrpB genes,. ECF sigma 70 factor (hrpL) gene, ,rpoD gene for RNA polymerase sigma factor, strain NCPPB 2096,rpoB gene for RNA polymerase beta subunit, strain CFBP 1731)
  • Pseudomonas syringae pv. magnoliae( 4 gene): hrpS, hrpA, hrpZ, hrpB genes
  • Pseudomonas syringae pv. panici( 5 genes) (tpmE) gene, partial cds, i CFBP2345 ECF sigma 70 factor (hrpL) gene, complete cds,rpoB gene for RNA polymerase beta subunit, strain CFBP 2345
  • Pseudomonas syringae pv. papulans( 8 genes ): CFBP1754 ECF sigma 70 factor (hrpL) gene, AvrPto1 gene, ICMP 4044 16S ribosomal RNA gene, ICMP 4048 16S-23S ribosomal RNA ,16S-23S ribosomal RNA ,rpoD gene for RNA , rpoB gene for RNA
  • Pseudomonas syringae pv. pisi(complete genome )
  • Pseudomonas syringae pv. syringae (complete genome)
  • Pseudomonas syringae pv. theae (complete genome)
  • Pseudomonas syringae RM.P20 (complete genome)
  • Pseudomonas syringae RM.P66 (complete genome)
  • Pseudomonas syringae RMX.24.a.1 (complete genome)
  • Pseudomonas syringae RMX815.1a (complete genome)
  • Pseudomonas syringae group pathovars incertae sedis
  • Pseudomonas syringae group genomosp. 2
  • Pseudomonas amygdali
  • Pseudomonas syringae pv. aesculi (complete genome)
  • Pseudomonas syringae pv. ciccaronei ( 8 genes):partial cds, p2342A RepA (repA) gene, complete cds,p2342A TraY (traY) gene, partial cds,p2342A B0046 protein gene, partial cds,2342 RpoD (rpoD) gene, partial cds,GyrB (gyrB) gene, partial cds,rpoD gene for RNA polymerase sigma factor, strain NCPPB 2355,rpoB gene for RNA
  • Pseudomonas syringae pv. dendropanacis ( 9 genes). hrpS, hrpA, hrpZ, hrpB genes, complete and partial cds, strain: kakuremino-1, psvA gene for PsvA protein, complete cds, rpoD gene , rpoB gene for RNA polymerase beta subunit, strain CFBP 3226
  • Pseudomonas syringae pv. eriobotryae(11 genes): hrpS, hrpA, hrpZ, hrpB genes, complete and partial cds, strain: PERB8031, ISPsy2 DNA, sequence ISPsy3 gene f,rpoD gene, strain NCPPB 2331, gene for 16S rRNA,rpoB gene
  • Pseudomonas syringae pv. hibisci( 2 genes):partial rpoD gene for RNA strain NCPPB 3682 andrpoB gene for RNA polymerase beta subunit, strain CFBP 2895
  • Pseudomonas syringae pv. lachrymans (complete genome)
  • Pseudomonas syringae pv. mellea (10 genes):HopZ3 gene, complete cds,sigma 70 factor (rpoD) gene, rpoD-26 allele, glucose-6-phosphate isomerase (pgi) gene, pgi-13 allele, partial cds, gyrase B (gyrB) gene, gyrB-5 allele, partial cds, citrate synthase I (gltA) gene, gltA-13 allele, partial cds,N6801 glyceraldehyde-3-phosphate dehydrogenase (gap1) gene, gap1-8 allele, partial cds, 1-phosphofructokinase (fruK) gene, fruK-18 allele, partial cds,aconitase B (acnB) gene, acnB-7 allele, partial cds,partial rpoD gene for RNA,partial rpoB gene for RNA, strain CFBP 2344
  • Pseudomonas syringae pv. mori (complete genome)
  • Pseudomonas syringae pv. morsprunorum (complete genome)
  • Pseudomonas syringae pv. myricae (20 genes): hrpS, hrpA, hrpZ, hrpB genes. sigma 70 factor (rpoD) gene, rpoD-23 allele, partial cds,AZ 84488 glucose-6-phosphate isomerase (pgi) gene, pgi-15 allele, partial cds,Z 84488 gyrase B (gyrB) gene, gyrB-19 allele, partial cds,e I (gltA) gene, gltA-12 allele, partial cds,glyceraldehyde-3-phosphate dehydrogenase (gap1) gene, gap1-4 allele, partial cds,phosphofructokinase (fruK) gene, fruK-13 allele, partial cds,aconitase B (acnB) gene, acnB-3 allele, partial cds,1 sigma 70 factor (rpoD) gene, rpoD-23 allele,,02941 glucose-6-phosphate isomerase (pgi) gene,302941 gyrase B (gyrB) gene, gyrB-19 allele, 302941 citrate synthase I (gltA) gene, gltA-12 allele,glyceraldehyde-3-phosphate dehydrogenase (gap1) gene, gap1-4 allele, MAFF 302941 1-phosphofructokinase (fruK) gene, fruK-13 allele, partial cds,MAFF 302941 aconitase B (acnB) gene, acnB-3 allele, psvA gene for PsvA protein, MAFF302941 effector AvrPto3 gene, partial rpoD gene for RNA polymerase sigma factor, strainDNA for 16S rRNApartial rpoB gene
  • Pseudomonas syringae pv. photiniae(2 genes): rpoD gene for RNA polymerase sigma factor, strain NCPPB 3688, rpoB gene for RNA polymerase beta subunit, strain CFBP 2899
  • Pseudomonas syringae pv. sesami(10 genes): hrpS, hrpA, hrpZ, hrpB genes, complete and partial cds, strain: PSES-1,HC_1 hopZ1 pseudogene, complete sequence, HC-1 type III effector HopZ2, ethylene-forming enzyme (efe) gene, complete cds (hopZ2) gene, rpoD gene for RNA polymerase sigma factor, strain, rpoB gene for RNA
  • Pseudomonas syringae pv. tabaci(complete genome)
  • Pseudomonas syringae pv. ulmi (3 genes):P 16S-23S ribosomal RNA intergenic spacer, partial sequence-rpoD gene for RNA polymerase sigma factor, strain NCPPB 632,rpoB gene for RNA polymerase beta subunit, strain CFBP 1407-
  • Pseudomonas syringae pv. coryli
  • Pseudomonas syringae group genomosp. 3
  • Pseudomonas syringae pv. antirrhini(13genes): (gltA) gene, gltA-ST1 allele, partial cds, (kup) gene, kup-ST1 allele,126 hypothetical protein gene, partial cds,70 factor (rpoD) gene, rpoD-ST1 allele, partial cds, gyrase B (gyrB) gene, gyrB-ST1 allele, partial cds,70 factor (rpoD) gene, rpoD-ST1 allele, partial cds--gyrase B (gyrB) gene, gyrB-ST1 allele, partial, uptake protein and hypothetical protein genes, partial cds,-6-phosphate isomerase (pgi) gene, pgi-ST1 allele, partial cds,-6-phosphate isomerase (pgi) gene, pgi-ST1 allele, partial cds, glyceraldehyde-3-phosphate dehydrogenase (gap1) gene, gap1-ST1 allele, partial cds, 4303 16S-23S ribosomal RNA intergenic spacer, partial sequence,rpoD gene for RNA polymerase sigma factor, strain NCPPB 1817,rpoB gene for RNA polymerase beta subunit, strain CFBP 1660
  • Pseudomonas syringae pv. antirrhini str. 126(8 genes):(gltA) gene, gltA-ST1 allele, partial cds,(kup) gene, kup-ST1 allele, partial cds,hypothetical protein gene, partial cds,(rpoD) gene, rpoD-ST1 allele, partial cds, DNA gyrase B (gyrB) gene, gyrB-ST1 allele, partial cds,putative potassium uptake protein and hypothetical protein genes, partial cds, glucose-6-phosphate isomerase (pgi) gene, pgi-ST1 ,3-phosphate dehydrogenase (gap1) gene, gap1-ST1 allele, partial cds
  • Pseudomonas syringae pv. apii( 18 genes). 16S ribosomal RNA gene, D protein (avrD) gene, (kup) gene, kup-ST8 allele, partial cds,gyrase B (gyrB) gene, gyrB-ST6 allele, partial cds, hypothetical protein gene, partial cds, B (acnB) gene, acnB-ST2 allele, partial cds,glucose-6-phosphate isomerase (pgi) gene, pgi-ST6 allele, partial cds,uptake protein and hypothetical protein genes, partial cds, (rpoD) gene, rpoD-ST8 allele, partial,212 internal transcribed spacer 1, complete sequence, nternal transcribed spacer 1, complete sequence, RNA polymerase sigma factor, strain NCPPB-RNA polymerase sigma factor, strain NCPPB--hemolysin co-regulated ,l rpoB gene for RNA polymerase beta subunit, strain CFBP, p1089A partial repA gene, p1089A partial repA gene
  • Pseudomonas syringae pv. berberidis( 2 genes):rpoD gene for RNA polymerase sigma factor, strain NCPPB 2724, rpoB gene for RNA polymerase beta subunit, strain CFBP 1727
  • Pseudomonas syringae pv. delphinii( 9 genes): hrpS, hrpA, hrpZ, hrpB genes,: 16S-23S ribosomal RNA --rpoD gene r, strain NCPPB 1879--HRP PATHOGENICITY ISLAND AND THEIR USES, rpoB gene for RNA polymerase beta subunit, strain CFBP 2215
  • Pseudomonas syringae pv. maculicola (complete genome)
  • Pseudomonas syringae pv. maculicola str. ES4326 (906 genes)
  • Pseudomonas syringae pv. maculicola str. F1( 6 genes):F1 glyceraldehyde-3-phosphate dehydrogenase (gap1) gene, gap1-ST5 allele, partial cds,F1 putative potassium uptake protein (kup) gene, kup-ST5 allele, partial cds, F1 DNA gyrase B (gyrB) gene, gyrB-ST5 allele, partial cds, B (acnB) gene, acnB-ST6 allele, partial cds--6-phosphate isomerase (pgi) gene, pgi-ST5 allele, partial cds
  • Pseudomonas syringae pv. maculicola str. M3( 5 genes):gyrase B (gyrB) gene, gyrB-ST8 allele, partial cds, uptake protein and hypothetical protein genes, partial cds, (rpoD) gene, rpoD-ST7 allele, partial cds, (acnB) gene, acnB-ST4 allele, partial cds, HopI1 (hopI1) gene, partial cds
  • Pseudomonas syringae pv. maculicola str. M6 (17 genes): pFKN, complete sequence--plasmid pFKN, complete sequence-, M6 AvrPphE pathogenicity islet,M6 DNA gyrase B (gyrB) gene, gyrB-ST4 allele, partial cds--M6 putative potassium uptake protein and hypothetical protein genes, partial cds, aconitase B (acnB) gene, acnB-ST5 allele, partial cds, glucose-6-phosphate isomerase (pgi) gene, pgi-ST3 , (kup) gene, kup-ST7 allele, partial cds, sigma 70 factor (rpoD) gene, rpoD-ST5 allele,70 factor (rpoD) gene, rpoD-5 allele, partial cds, glucose-6-phosphate isomerase (pgi) gene, pgi-20 allele, partial cds, gyrase B (gyrB) gene, gyrB-24 , (gltA) gene, gltA-4, g (gap1) gene, (fruK) gene, B (acnB) gene, acnB-13 a, HopI1 (hopI1) gene,
  • Pseudomonas syringae pv. passiflorae(5 genes): (rpoD) gene, 16S-23S ri, 23S ribosomal RNA gene, p tRNA-Ile and tRNA-Ala genes, crpoD gene f, rpoB gene fo
  • Pseudomonas syringae pv. persicae. (8 genes): (rpoD) gene, RepA (repA) gene, , sGyrB (gyrB) gene, sTraY (traY) gene, QueA gene, p; tRNA-Leu gene,; HrpK gene, partials--rpoD gene f, rpoB gene
  • Pseudomonas syringae pv. philadelphi. rpoD gene and rpoB gene
  • Pseudomonas syringae pv. primulae. rpoD gene and rpoB gene
  • Pseudomonas syringae pv. ribicola. rpoD gene and rpoB gene for RNA
  • Pseudomonas syringae pv. tomato(complete genome)
  • Pseudomonas syringae pv. tomato K40(complete genome)
  • Pseudomonas syringae pv. tomato Max13(complete genome)
  • Pseudomonas syringae pv. tomato NCPPB 1108 (complete genome)
  • Pseudomonas syringae pv. tomato str. DC3000 (complete genome)
  • Pseudomonas syringae pv. tomato str. JL1065. (6 genes):(shcM) and HopM1 (hopM1) genes, hypothetical protein gene, p, glucose-6-phosphate isomerase (pgi) gene, (rpoD) gene, rpoD, (kup) gene ,AvrPtoB (avrPtoB) gene, avrRpt2 gene
  • Pseudomonas syringae pv. tomato T1(complete genome)
  • Pseudomonas syringae pv. viburni
  • Pseudomonas syringae group genomosp. 7 rpoD gene ,rpoB gene
  • Pseudomonas syringae pv. helianthi.16S-23Sgene, rpoD gene andrpoB gene
  • Pseudomonas syringae pv. tagetis. (asnB) gene and16S-23S gene

We also considered MLSA database in our bioinformatic analysis. This database includes various genes that are used for the detection of bacteria. The greatest challenge of using these genes for detection purposes in P.syringae is that when we perform BLAST by these genes, in addition to the P.syringae strains, they can detect other species of the genus Pseudomonas as well the species belonging to other genera.

We did not solely rely on the sequence analysis of hrcV in NCBI and extended the investigation of the hrcV sequence to other databases including DDBJ (DNA Data Bank of Japan), EMBL (European Molecular Biology Laboratory) and PAIDB (PAthogenicity Islands Data Base). The analyses performed by using these databanks were in accordance with the results as those obtained from analysis in NCBI.