<p>Table S3. Pseudogenes in C. rodentium ICC168</p><p>CDS ID Gene Predicted product Note ROD_01891 putative polysaccharide degrading enzyme pseudogene, disrupted by ISCro1 insertion (pseudogene) ROD_02031 ISCro6 transposase (pseudogene) pseudogene, truncated by frameshift mutation ROD_02381 lfiG lateral flagellar C-ring switch protein pseudogene, C-terminus missing, truncated by prophage (fragment) CRP28 insertion ROD_02721 hypothetical prophage protein pseudogene, disrupted by ISCro3 insertion. (pseudogene) ROD_02841 hypothetical prophage protein (fragment) pseudogene, C-terminus missing, truncated by IS102 insertion ROD_02951 lfiI lateral flagellar export/assembly protein pseudogene, N-terminus missing, truncated by prophage (fragment) CRP28 insertion ROD_03001 putative glysosyltransferase (pseudogene) pseudogene, truncated by premature stop codon ROD_03091 lfgF lateral flagellar rod protein (pseudogene) pseudogene, truncated by premature stop codon ROD_03411 IS3 family transposase B (pseudogene) pseudogene, N-terminus missing, C-terminal part truncated by premature stop codon ROD_03432 putative transposase (fragment) pseudogene, N-terminus missing, C-terminal part truncated by frameshift mutations ROD_05231 putative transposase (pseudogene) pseudogene, disrupted by IS102 insertion ROD_05661 pheP phenylalanine-specific permease pseudogene, truncated by premature stop codon (pseudogene) ROD_05781 transposase (pseudogene) pseudogene, disrupted by ISEc14 insertion and an internal deletion. ROD_38701 is an intact copy of this transposase, and is also found adjacent to NleD ROD_05861 putative sugar ABC transporter, pseudogene, truncated by frameshift mutation periplasmic protein precursor (pseudogene) ROD_05881 glycerol kinase (pseudogene) pseudogene, truncated by premature stop codon ROD_06421 ISCro6 transposase (pseudogene) pseudogene, disrupted by ISCro1 insertion ROD_06641 rihA pyrimidine-specific ribonucleoside pseudogene, truncated by premature stop codon hydrolase (pseudogene) ROD_07161 pcp pyrrolidone-carboxylate peptidase pseudogene, C-terminus missing, truncated by downstream (fragment) deletion event ROD_07162 nei Endonuclease VIII (fragment) pseudogene, N-terminus missing, truncated by upstream deletion event ROD_08491 mdfA multidrug translocase MdfA (pseudogene) pseudogene, truncated by frameshift mutation ROD_08971 large repetitive protein (pseudogene) pseudogene, probable type I secreted protein, disrupted by prophage CRP99 insertion ROD_08982 putative phage tail fibre protein pseudogene, alternative tail fibre tip, disrupted by ISCro1 (pseudogene) insertion ROD_10341 putative phage integrase (pseudogene) pseudogene, fragmented by two frameshifts and N-terminal deleted by ISCro1 insertion ROD_10431 putative integrase (fragment) pseudogene, N-terminus missing, fragment ROD_10521 putative adhesin autotransporter pseudogene, truncated by frameshift mutation (pseudogene) ROD_10522 IS200 family transposase (fragment) pseudogene, C-terminus missing, fragment ROD_10751 phoH phosphate starvation-inducible protein pseudogene, truncated by frameshift mutation PhoH (pseudogene) ROD_10762 putative integrase (fragment) pseudogene, C-terminus missing, fragment ROD_10771 putative DNA helicase (fragment) pseudogene, N- and C-termini missing, fragment ROD_10791 IS200 family transposase (pseudogene) pseudogene, fragmented by multiple mutations. Lacking start codon due to missense mutation at N-terminus, also truncated by frameshift mutation and premature stop codon ROD_10801 ISCro3 transposase (fragment) pseudogene, N-terminal 165aa of ISCro3 transposase, fragment ROD_10811 IS200 family transposase (fragment) pseudogene, N-terminal 40 aa missing, fragment ROD_10821 ISCro3 transposase (fragment) pseudogene, N- and C-termini missing, fragment. aa 283 to 422 of ISCro3 transposase. Terminal 23 aa of the transposase are missing, part of N-terminus is upstream of adjacent IS200-family IS element fragment ROD_10851 putative IS21 family transposase pseudogene, truncated by frameshift mutation and (pseudogene) premature stop codon ROD_10891 conserved hypothetical protein pseudogene, truncated by two frameshift mutations (pseudogene) ROD_11261 mdtH multidrug resistance protein MdtH pseudogene, truncated by frameshift mutation (pseudogene) ROD_11301 putative oxidoreductase (pseudogene) pseudogene, truncated by frameshift mutation ROD_11371 flgN flagella synthesis protein FlgN pseudogene, disrupted by ISCro3 insertion (pseudogene) ROD_11411 flgC flagellar basal-body rod protein FlgC pseudogene, C-terminus missing, truncated by downstream (fragment) deletion ROD_11412 flgJ peptidoglycan hydrolase FlgJ pseudogene, N-terminus missing, truncated by upstream (pseudogene) deletion ROD_11741 putative tonB-dependent receptor pseudogene, N-terminus missing, fragment (fragment) ROD_12051 putative tail fiber protein (pseudogene) pseudogene, truncated by frameshift mutation ROD_12081 espN1 putative T3SS effector protein EspN1 pseudogene, fragmented by two frameshift mutations and a (pseudogene) premature stop codon ROD_12851 putative transport protein (pseudogene) pseudogene, disrupted by ICSCro1 insertion ROD_13611 putative Rhs protein (fragment) pseudogene, N-terminus missing, fragment ROD_13871 putative ABC transporter, inner membrane pseudogene, N-terminus missing, fragment protein (fragment) ROD_14811 rspB starvation-sensing protein RspB pseudogene, N-terminus missing, fragment (fragment) ROD_15501 putative CoA-transferase beta subunit pseudogene, C-terminus missing, truncated by downstream (fragment) deletion event ROD_15511 putative citrate transporter (fragment) pseudogene, N-terminus missing, truncated by upstream deletion event and C-terminal part truncated by frameshift mutation ROD_15781 TonB-dependent receptor (pseudogene) pseudogene, truncated by frameshift mutation ROD_16201 putative virulence protein (pseudogene) pseudogene, truncated by frameshift mutation ROD_16492 nleB2 putative T3SS effector protein NleB2 pseudogene, truncated by frameshift mutation and internal (pseudogene) deletion ROD_16501 putative tail fibre protein (fragment) pseudogene, N-terminus missing, fragment ROD_16541 putative transposase A (fragment) pseudogene, N-terminal missing, truncated by ISEc14 insertion ROD_16542 putative transposase B (fragment) pseudogene, C-terminus missing, fragment ROD_16561 putative prophage integrase (pseudogene) pseudogene, fragmented by multiple frameshift mutations ROD_16911 putative sugar ABC transporter, ATP- pseudogene, truncated by premature stop codon binding protein (pseudogene) ROD_17541 TonB-dependent outer membrane pseudogene, disrupted by ISCro3 insertion siderophore receptor (pseudogene) ROD_19101 retA putative reverse transcriptase/maturase pseudogene, N-terminus missing, C-terminal part (pseudogene) fragmented by two frameshift mutations ROD_19121 trpA tryptophan synthase alpha chain pseudogene, N- and C-termini missing, fragmented by two (pseudogene) frameshift mutations ROD_19261 Rhs protein (pseudogene) pseudogene, C-terminus missing, N-terminal part truncated by frameshift mutation ROD_19521 araG arabinose import ATP-binding protein pseudogene, truncated by frameshift mutation AraG (pseudogene) ROD_20071 fliC flagellin pseudogene, disrupted by prophage CRP20 insertion ROD_20531 conserved hypothetical protein pseudogene, truncated by premature stop codon (pseudogene) ROD_20721 Rhs protein (fragment) pseudogene, N-terminus missing, fragment ROD_21471 putative membrane protein (pseudogene) pseudogene, truncated by frameshift mutation ROD_22471 putative polygalacturonase (pseudogene) pseudogene, truncated by premature stop codon ROD_22621 dusC tRNA dihydrouridine synthase C pseudogene, truncated by premature stop codon (pseudogene) ROD_23641 putative Rhs protein (fragment) pseudogene, N-terminus deleted by ISCro1, fragment ROD_23781 ptsJ putative transcriptional regulator, GntR pseudogene, truncated by frameshift mutation family (pseudogene) ROD_24181 acrD putative multidrug efflux pump pseudogene, truncated by premature stop codon (pseudogene) ROD_24371 conserved hypothetical protein (fragment) pseudogene, C-terminus missing, fragment ROD_24381 conserved hypothetical protein (fragment) pseudogene, N-terminus missing, fragment ROD_24621 pbpC penicillin-binding protein 1C pseudogene, truncated by frameshift mutation (pseudogene) ROD_26351 prophage CP4-57 integrase (fragment) pseudogene, C-terminus missing, truncated by ISEc14 insertion ROD_26391 IS3 family transposase A (fragment) pseudogene, C-terminus deleted by another IS3 family IS element ROD_26491 Rhs protein (pseudogene) pseudogene, C-terminus deleted by ISCro1 insertion, N- terminal part fragmented by frameshift mutation and premature stop codon ROD_26751 rnz ribonuclease Z (tRNA endonuclease) pseudogene, truncated by premature stop codon (pseudogene) ROD_27502 putative integrase (fragment) pseudogene, C-terminus missing, fragment ROD_27701 cts1I IcmF family T6SS protein Cts1I IcmF component of T6SS. Has a frameshift but may be functional as the frameshift occurs at a poly A tract ROD_28201 Rhs protein (pseudogene) pseudogene, C-terminus missing, N-terminal part fragmented by frameshift mutation and premature stop codon ROD_28261 hypothetical protein (fragment) pseudogene, N-terminus deleted by ISCro1 insertion ROD_28291 putative Rhs protein (fragment) pseudogene, N-terminus missing, C-terminus deleted by ISCro1 insertion ROD_28941 putative exported protein (pseudogene) pseudogene, disrupted by IS102 insertion ROD_29351 putative fimbrial subunit (pseudogene) pseudogene, truncated by premature stop codon ROD_29421 putative integrase (fragment) pseudogene, N- and C-termini missing, also truncated by frameshift mutation ROD_29461 hypothetical protein (pseudogene) pseudogene, C-terminus missing, truncated by IS102 insertion ROD_29641 putative transposase (pseudogene) pseudogene, N-terminal deleted by ISEc14 insertion, C- terminal part fragmented by three frameshift mutations ROD_29811 IS256 family transposase (pseudogene) pseudogene, fragmented by five frameshift mutations and two premature stop codons ROD_30031 putative transposase (pseudogene) pseudogene, fragmented by six frameshift mutations and a premature stop codon ROD_30221 truC tRNA pseudouridine synthase C pseudogene, truncated by premature stop codon (pseudogene) ROD_31521 putative anti-adapter protein IraM pseudogene, C-terminus deleted by IS102 insertion (pseudogene) ROD_31701 hypothetical protein (pseudogene) pseudogene, N-terminus missing, C-terminal part truncated by frameshift mutation ROD_31741 putative tail fibre protein (pseudogene) one of three copies of this protein in CR (ROD_12061, ROD_16501, ROD_31741) ROD_31761 nleG2 putative T3SS effector protein NleG2 pseudogene, truncated by premature stop codon and (pseudogene) frameshift mutation ROD_31781 nleG putative T3SS effector protein NleG pseudogene, fragmented by two premature stop codons and (pseudogene) three frameshift mutations ROD_31801 IS66 family transposase B (pseudogene) pseudogene, truncated by frameshift mutation ROD_31831 IS3 family transposase B (fragment) pseudogene, N-terminus missing, C-terminal part fragmented by three frameshift mutations ROD_31851 espN2- putative T3SS effector protein EspN2-1 pseudogene, truncated by two frameshift mutations and 1 (pseudogene) missense mutation of start codon ROD_31861 putative transposase (pseudogene) pseudogene, truncated by frameshift mutation ROD_31951 putative DNA binding protein pseudogene, truncated by frameshift mutation (pseudogene) ROD_31961 putative integrase (pseudogene) pseudogene, truncated by frameshift mutation and premature stop codon ROD_32771 putative oxidoreductase (pseudogene) pseudogene, truncated by premature stop codon ROD_33321 putative integrase (pseudogene) pseudogene, truncated by frameshift mutation ROD_33391 hypothetical protein (pseudogene) pseudogene, disrupted by IS102 insertion ROD_33451 conserved hypothetical protein pseudogene, truncated by frameshift mutation and (pseudogene) premature stop codon ROD_33471 traU putative conjugative transfer system pseudogene, N-terminus missing, fragment protein TraU (fragment) ROD_33472 putative sulfatase (fragment) pseudogene, C-terminus missing, fragment ROD_33491 traB putative conjugative transfer system pseudogene, C-terminus missing, N-terminal part truncated protein TraB (fragment) by frameshift mutation ROD_33511 conserved hypothetical protein pseudogene, N-terminus missing due to start codon (pseudogene) mutation, truncated by frameshift mutation ROD_33591 putative membrane protein (pseudogene) pseudogene, truncated by premature stop codon ROD_33611 traD putative conjugative transfer system pseudogene, N-terminus missing, C-terminal part truncated protein TraD (fragment) by frameshift mutation ROD_33621 traW putative conjugative transfer system pseudogene, N-terminus missing, fragment protein TraW (fragment) ROD_33622 traL putative conjugative transfer system pseudogene, C-terminus missing, fragment protein TraL (fragment) ROD_33651 pilL putative Type IV pilus protein (fragment) pseudogene, C-terminus missing, fragment ROD_33771 conserved hypothetical protein pseudogene, truncated by frameshift mutation (pseudogene) ROD_33841 IS3 family transposase B (fragment) pseudogene, N-terminus deleted by ISEc14 insertion, C- terminus missing, remaining fragment truncated by premature stop codon ROD_34121 cts2I IcmF family T6SS protein Cts2I pseudogene, truncated by frameshift mutation (pseudogene) ROD_34312 IS200 family transposase (fragment) pseudogene, N-terminus deleted by ISCro1 insertion ROD_34381 fecR putative regulator for fec operon FecR pseudogene, fragmented by approx 150 aa deletion and (fragment) frameshift mutation ROD_34911 anaerobic dimethyl sulfoxide reductase pseudogene, truncated by frameshift mutation chain (pseudogene) ROD_35291 conserved hypothetical protein pseudogene, C-terminus deleted by ISCro1 insertion (pseudogene) ROD_35341 putative Rhs protein (pseudogene) pseudogene, N-terminus deleted by ISCro1 insertion, C- terminal part truncated by frameshift mutation ROD_35381 putative glutathione S-transferase pseudogene, fragmented by 100 aa deletion and frameshift (pseudogene) mutation ROD_35471 methyl-accepting chemotaxis protein pseudogene, fragmented by 225 aa deletion and two (fragment) frameshift mutations ROD_35581 AraC-family transcriptional regulator pseudogene, truncated by premature stop codon (pseudogene) ROD_35741 putative sugar transporter (pseudogene) pseudogene, truncated by frameshift mutation ROD_36221 IS200 family transposase (fragment) pseudogene, C-terminus deleted by ISCro1 insertion ROD_36261 ISCro6 transposase (pseudogene) pseudogene, truncated by frameshift mutation ROD_36451 conserved hypothetical protein pseudogene, disrupted by prophage CRP38 insertion (pseudogene) ROD_37911 AraC-family transcriptional regulator pseudogene, truncated by premature stop codon (pseudogene) ROD_39811 Putative magnesium chelatase pseudogene, truncated by premature stop codon (pseudogene) ROD_40661 Rhs protein (pseudogene) pseudogene, fragmented by two frameshift mutations and ISCro1 insertion ROD_40741 Rhs protein (fragment) pseudogene, N-terminus missing, fragment ROD_40761 conserved hypothetical protein (fragment) pseudogene, N-terminus missing, C-terminal part truncated by frameshift mutation and premature stop codon ROD_40772 putative transposase (fragment) pseudogene, N- and C-termini missing, truncated by frameshift mutation ROD_40773 ISCro3 transposase (fragment) pseudogene, N-terminus missing, fragment ROD_40781 intimin-like protein (pseudogene) pseudogene, truncated by frameshift mutation ROD_40831 putative transposase (pseudogene) pseudogene, truncated by two frameshift mutations ROD_40861 espM1 putative T3SS effector protein EspM1 pseudogene, fragmented by three premature stop codons and a frameshift mutation ROD_40961 IS3 family transposase B (fragment) pseudogene, N- and C-termini missing, truncated by frameshift ROD_40991 putative IS4 family transposase pseudogene, truncated by premature stop codon (pseudogene) ROD_41061 traX F pilin acetylation protein TraX (fragment) pseudogene, N- and C-termini missing, fragment ROD_41081 finO fertility inhibition protein (conjugal pseudogene, fragmented by two frameshift mutations and a transfer repressor)(pseudogene) premature stop codon ROD_41121 conserved hypothetical protein (fragment) pseudogene, N-terminal 30 aa missing, fragment ROD_41571 putative lytic transglycosylase (fragment) pseudogene, N-terminus missing, fragment ROD_41701 putative membrane protein (pseudogene) pseudogene, truncated by premature stop codon ROD_42151 lldD L-lactate dehydrogenase (pseudogene) pseudogene, fragmented by internal deletion and frameshift mutation ROD_42581 tag 3-methyladenine DNA glycosylase I pseudogene, truncated by frameshift mutation (pseudogene) ROD_42871 conserved hypothetical protein pseudogene, truncated by two frameshift mutations (pseudogene) ROD_42901 conserved hypothetical protein pseudogene, fragmented by internal deletion and frameshift (pseudogene) mutation ROD_43031 putative oligopeptide transporter pseudogene, truncated by premature stop codon (pseudogene) ROD_43081 putative exported protein (pseudogene) pseudogene, truncated by premature stop codon ROD_45781 Rhs protein (pseudogene) pseudogene, truncated by two frameshift mutations ROD_46891 gatD galactitol-1-phosphate dehydrogenase pseudogene, disrupted by prophage CRP49 insertion (pseudogene) ROD_47721 conserved hypothetical protein (fragment) pseudogene, N-terminal 150 aa missing, fragment ROD_47791 IS3 family transposase B (fragment) pseudogene, N-terminus missing, fragment ROD_47801 IS21 family transposase B (fragment) pseudogene, N-terminus missing, C-terminal part truncated by premature stop codon ROD_47821 IS3 family transposase A (fragment) pseudogene, C-terminus missing, N-terminal part truncated by premature stop codon ROD_47831 IS3 family transposase B (fragment) pseudogene, N-terminus missing, C-terminal part truncated by premature stop codon ROD_47841 putative transposase (fragment) pseudogene, N- and C-termini missing, additionally fragmented by premature stop codon and frameshift mutation ROD_47941 exuT hexuronate transporter (pseudogene) pseudogene, truncated by frameshift mutation ROD_48171 large repetitive protein (pseudogene) pseudogene, truncated by premature stop codon ROD_48761 putative integrase (fragment) pseudogene, C-terminus deleted by ISEc14 insertion, N- terminal part truncated by premature stop codon ROD_48791 IS3 family transposase B (fragment) pseudogene, C-terminus deleted by ISEc14 insertion ROD_48851 conserved hypothetical protein (fragment) pseudogene, C-terminus missing, missense mutation of the start codon, additionally fragmented by frameshift mutation and premature stop codon ROD_48921 conserved hypothetical protein pseudogene, fragmented by premature stop codon and three (pseudogene) frameshift mutations ROD_48941 IS3 family transposase B (pseudogene) pseudogene, fragmented by four premature stop codons ROD_48951 IS3 family transposase A (pseudogene) pseudogene, truncated by two frameshift mutations ROD_49201 conserved hypothetical protein pseudogene, truncated by premature stop codon (pseudogene) ROD_49321 bglA 6-phospho-beta-glucosidase (pseudogene) pseudogene, truncated by frameshift mutation ROD_49561 hypothetical protein (pseudogene) pseudogene, C-terminus missing, N-terminal part fragmented by three frameshift mutations ROD_49611 putative integrase (fragment) pseudogene, C-terminus missing, N-terminal part truncated by frameshift mutation ROD_49621 conserved hypothetical protein pseudogene, truncated by premature stop codon (pseudogene) ROD_49851 conserved hypothetical protein pseudogene, truncated by frameshift mutation (pseudogene) ROD_50031 conserved hypothetical protein Pseudogene, truncated by premature stop codon (pseudogene) ROD_50161 ISEc23 transposase C (fragment) pseudogene, N-terminus missing, probably deleted by ISCro1 insertion ROD_50162 ISCro1 transposase (fragment) pseudogene, N-terminus missing, fragment ROD_50181 IS4 transposase (fragment) pseudogene, N-terminus deleted by ISCro1 insertion ROD_50191 ISCro1 transposase (fragment) pseudogene, N-terminus missing, fragment ROD_50631 putative fimbrial usher protein (fragment) pseudogene, C-terminus deleted by IS102 insertion ROD_50651 putative fimbrial adhesin (fragment) pseudogene, N-terminus deleted by IS102 insertion ROD_p1151 putative IS256 family transposase pseudogene, C-terminus missing, N-terminal region (fragment) truncated by frameshift mutation ROD_p1261 conserved hypothetical plasmid protein pseudogene, N-terminus missing, C-terminal region (pseudogene) truncated by frameshift mutation ROD_p1291 putative fimbrial chaperone (fragment) pseudogene, N-terminus missing, fragment ROD_p1541 putative plasmid replication initiation pseudogene, N-terminus deleted by ISCro1 insertion, C- protein (pseudogene) terminal region truncated by frameshift mutation ROD_p1581 conserved hypothetical protein (fragment) pseudogene, N-terminus deleted by ISCro1 insertion ROD_p2461 triD putative conjugal transfer protein TriD pseudogene, disrupted by IS102 insertion (pseudogene) </p>