Figure S1. Pangenome plots of ten recombining bacterial species based on RAST annotated

Transcription

1 Figure S1

2 Figure S2

3 Supplementary Figure legends Figure S1. Pangenome plots of ten recombining bacterial species based on RAST annotated genomes. To generate these plots all strains within a species were annotated using the RAST annotation webserver and the pangenomes were generated as described above. Two plots are provided for each species: Left: HGT-artifact corrected pangenome plot the protein pangenome was compared to the full DNA sequences of the strains from which it was generated. Pangenes appearing in less than 50% of strains within a species at the annotated protein level, but in more than 75% of the strains at the whole DNA level, were removed from the plot; Right: Protein length corrected pangenome plot for each pangene within the HGT-artifact corrected pangenome lengths of all genes within the pangene group were compared to the length of the longest gene within the group. Genes, whose length was shorter than two thirds of the longest gene length, were removed from the pangene cluster and the pangene distribution was re-drawn. Figure S2. Pangenome plots of four clonal bacterial species based on RAST annotated genomes. To generate these plots all strains within a species were annotated using the RAST annotation webserver and the pangenomes were generated as described above. Two plots are provided for each species: Left: HGT-artifact corrected pangenome plot the protein pangenome was compared to the full DNA sequences of the strains from which it was generated. Pangenes appearing in less than 50% of strains within a species at the annotated protein level, but in more than 75% of the strains at the whole DNA level, were removed from the plot; Right: Protein length corrected pangenome plot for each pangene within the HGT-artifact corrected pangenome lengths of all genes within the pangene group were compared to the length of the longest gene within the group. Genes, whose length was shorter than two thirds of the longest gene length, were removed from the pangene cluster and the pangene distribution was re-drawn.

4 Table S1. Investigated strains and the percentage of near core pangenes absent from each strain Bacilllus cereus genes a lost genes b NC_ Bacillus cereus ATCC NC_ Bacillus cereus ATCC NC_ Bacillus cereus E33L NC_ Bacillus cereus AH NC_ Bacillus cereus B NC_ Bacillus cereus G NC_ Bacillus cereus AH NC_ Bacillus cereus Q NC_ Bacillus cereus 03BB NC_ Bacillus cereus biovar anthracis str. CI NC_ Bacillus cereus NC NC_ Bacillus cereus F837/ NC_ Bacillus cereus FRI Campylobacter jejuni Number of Percent of lost genes genes NC_ Campylobacter jejuni RM NC_ Campylobacter jejuni subsp. jejuni NC_ Campylobacter jejuni subsp. doylei NC_ Campylobacter jejuni subsp. jejuni NC_ Campylobacter jejuni subsp. jejuni ICDCCJ NC_ Campylobacter jejuni subsp

5 jejuni IA3902 NC_ Campylobacter jejuni subsp. jejuni M NC_ Campylobacter jejuni subsp. jejuni S NC_ Campylobacter jejuni subsp. jejuni NCTC BN148, NC_ Campylobacter jejuni subsp. jejuni PT NC_ Campylobacter jejuni subsp. jejuni NC_ Campylobacter jejuni subsp. jejuni NC_ Campylobacter jejuni Clostridium botulinum genes lost genes NC_ Clostridium botulinum A str. ATCC NC_ Clostridium botulinum A str. ATCC NC_ Clostridium botulinum A str. Hall NC_ Clostridium botulinum F str. Langeland NC_ Clostridium botulinum B1 str. Okra NC_ Clostridium botulinum A3 str. Loch Maree NC_ Clostridium botulinum A2 str. Kyoto NC_ Clostridium botulinum Ba4 str

6 NC_ NC_ Accession number NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ Clostridium botulinum F str Clostridium botulinum H diphtheriae Strain Name genes lost genes diphtheriae NCTC diphtheriae diphtheriae INCA diphtheriae CDCE diphtheriae HC diphtheriae HC diphtheriae HC diphtheriae PW diphtheriae VA diphtheriae 31A diphtheriae BH diphtheriae C7 (beta) diphtheriae HC

7 Accession number NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ pseudotuberculosis Strain Name genes lost genes pseudotuberculosis FRC pseudotuberculosis 3/ pseudotuberculosis pseudotuberculosis P54B pseudotuberculosis pseudotuberculosis C pseudotuberculosis I pseudotuberculosis PAT pseudotuberculosis 42/02-A pseudotuberculosis CIP pseudotuberculosis 1/06-A pseudotuberculosis pseudotuberculosis pseudotuberculosis pseudotuberculosis Cp

8 Escherichia coli-shigella Group genes lost genes NC_ Escherichia coli str. K-12 substr. MG NC_ Escherichia coli O157:H7 str. EDL NC_ Escherichia coli O157:H7 str. Sakai NC_ Escherichia coli CFT NC_ Escherichia coli str. K-12 substr. W NC_ Escherichia coli UTI NC_ Escherichia coli NC_ Escherichia coli APEC O NC_ Escherichia coli HS NC_ Escherichia coli E24377A NC_ Escherichia coli ATCC NC_ Escherichia coli SMS NC_ Escherichia coli O157:H7 str. EC NC_ Escherichia coli SE NC_ Escherichia coli O127:H6 str. E2348/ NC_ Escherichia coli IAI NC_ Escherichia coli S NC_ Escherichia coli ED1a NC_ Escherichia coli NC_ Escherichia coli IAI NC_ Escherichia coli UMN NC_ Escherichia coli LF NC_ Escherichia coli BW NC_ Escherichia coli B str. REL

9 NC_ Escherichia coli BL21(DE3) NC_ Escherichia coli O157:H7 str. TW NC_ Escherichia coli O103:H2 str NC_ Escherichia coli O26:H11 str NC_ Escherichia coli O111:H- str NC_ Escherichia coli SE NC_ Escherichia coli O55:H7 str. CB NC_ Escherichia coli KO11FL NC_ Escherichia coli DH NC_ Escherichia coli NC_ Escherichia coli IHE NC_ Escherichia coli ABU NC_ Escherichia coli ETEC H NC_ Escherichia coli W NC_ Escherichia coli UMNK NC_ Escherichia coli O7:K1 str. CE NC_ Escherichia coli str. 'clone D i14' NC_ Escherichia coli O55:H7 str. RM NC_ Escherichia coli P12b NC_ Escherichia coli Xuzhou NC_ Escherichia coli O104:H4 str. 2009EL NC_ Escherichia coli O104:H4 str. 2011C NC_ Escherichia coli O104:H4 str

10 2009EL-2071 NC_ Escherichia coli APEC O NC_ Escherichia coli LY NC_ Escherichia coli PMV-1 main NC_ Escherichia coli JJ NC_ Shigella flexneri 2a str NC_ Shigella flexneri 2a str. 2457T NC_ Shigella sonnei Ss NC_ Shigella dysenteriae Sd NC_ Shigella boydii Sb NC_ Shigella flexneri 5 str NC_ Shigella boydii CDC NC_ Shigella sonnei 53G NC_ Shigella flexneri Francisella tularensis genes lost genes NC_ Francisella tularensis subsp. tularensis SCHU S NC_ Francisella tularensis subsp. holarctica LVS NC_ Francisella tularensis subsp. tularensis FSC NC_ Francisella tularensis subsp. holarctica OSU NC_ Francisella tularensis subsp. tularensis WY NC_ Francisella tularensis subsp. holarctica FTNF NC_ Francisella tularensis subsp. mediasiatica FSC NC_ Francisella tularensis TIGB NC_ Francisella tularensis subsp

11 tularensis TI0902 NC_ Francisella tularensis subsp. tularensis NE NC_ Francisella tularensis subsp. holarctica F NC_ Francisella tularensis subsp. holarctica FSC Haemophilus influenzae genes lost genes NC_ Haemophilus influenzae Rd KW NC_ Haemophilus influenzae NP NC_ Haemophilus influenzae PittEE NC_ Haemophilus influenzae PittGG NC_ Haemophilus influenzae F NC_ Haemophilus influenzae F NC_ Haemophilus influenzae NC_ Haemophilus influenzae R NC_ Haemophilus influenzae R NC_ Haemophilus influenzae KR genes lost genes NC_ serotype 4b str. F NC_ EGD-e NC_ HCC NC_

12 Clip81459 NC_ NC_ NC_ L NC_ M NC_ S NC_ J NC_ FSL R NC_ Finland NC_ ATCC NC_ SLCC NC_ SLCC NC_ SLCC NC_ SLCC NC_ SLCC NC_ SLCC NC_ serotype 7 str. SLCC NC_ SLCC NC_

13 SLCC7179 NC_ L NC_ serotype 4b str. LL NC_ J NC_ EGD Complex genes lost genes NC_ CDC NC_ Mycobacterium bovis AF2122/ NC_ Mycobacterium bovis BCG str. Pasteur 1173P NC_ H37Ra NC_ F NC_ Mycobacterium bovis BCG str. Tokyo NC_ KZN NC_ Mycobacterium africanum GM NC_ KZN NC_ Mycobacterium bovis BCG str. Mexico NC_ UT NC_ CCDC

14 NC_ NC_ NC_ NC_ NC_ NC_ NC_ NC_ Accession number CCDC CTRI KZN H37Rv complete genome Mycobacterium bovis BCG str. Korea 1168P str. Erdman = ATCC DNA str. Haarlem Neisseria meningitidis Strain Name genes lost genes NC_ Neisseria meningitidis MC NC_ Neisseria meningitidis Z NC_ Neisseria meningitidis FAM NC_ Neisseria meningitidis NC_ Neisseria meningitidis alpha NC_ Neisseria meningitidis NC_ Neisseria meningitidis alpha NC_ Neisseria meningitidis WUE NC_ Neisseria meningitidis G NC_ Neisseria meningitidis M

15 NC_ Neisseria meningitidis M NC_ Neisseria meningitidis H44/ NC_ Neisseria meningitidis M NC_ Neisseria meningitidis NZ- 05/ Pseudomonas aeruginosa genes lost genes NC_ Pseudomonas aeruginosa PAO NC_ Pseudomonas aeruginosa UCBPP-PA NC_ Pseudomonas aeruginosa PA7 chromosome NC_ Pseudomonas aeruginosa LESB NC_ Pseudomonas aeruginosa M NC_ Pseudomonas aeruginosa NCGM2.S NC_ Pseudomonas aeruginosa DK NC_ Pseudomonas aeruginosa B136-33, NC_ Pseudomonas aeruginosa RP NC_ Pseudomonas aeruginosa PA NC_ Pseudomonas aeruginosa MTB NC_ Pseudomonas aeruginosa LES NC_ Pseudomonas aeruginosa SCV

16 genes lost genes NC_ TIGR NC_ R NC_ D NC_ Hungary19A NC_ CGSP NC_ G NC_ ATCC NC_ JJA NC_ P NC_ NC_ Taiwan19F NC_ TCH8431/19A NC_ AP NC_ B NC_ INV NC_ OXC NC_ INV NC_

17 ST556 NC_ SPNA NC_ gampni NC_ A026 genome Yersinia pestis genes lost genes NC_ Yersinia pestis CO NC_ Yersinia pestis KIM NC_ Yersinia pestis biovar Microtus str NC_ Yersinia pestis Nepal NC_ Yersinia pestis Antiqua NC_ Yersinia pestis Pestoides F NC_ Yersinia pestis Angola NC_ Yersinia pestis Z NC_ Yersinia pestis D NC_ Yersinia pestis D NC_ Yersinia pestis A NC_ Yersinia pestis biovar Medievalis str. Harbin a Number of genes from each strain used for the construction of pangenomes (see Materials and Methods) b Percent of near core gene loss. Calculated as 100*L/T, where L is the number of near core core pangenes that are absent from the genome and T is the total number of genes present within that genome, that were used to construct the species pangenome.

18 Table S2. List of bacterial strains removed from our analysis Campylobacter jejuni Accession number Strain Name NC_ Campylobacter jejuni subsp. jejuni NCTC = ATCC NC_ Campylobacter jejuni subsp. jejuni NC_ Campylobacter jejuni subsp. jejuni NC_ Campylobacter jejuni Clostridium botulinum NC_ Clostridium botulinum B str. Eklund 17B NC_ Clostridium botulinum E3 str. Alaska E43 NC_ Clostridium botulinum BKT Escherichia coli-shigella Group NC_ Escherichia coli NA114 NC_ Escherichia coli UM146 NC_ Escherichia coli O83:H1 str. NRG 857C NC_ Shigella dysenteriae 1617 NC_ Escherichia coli str. K-12 substr. MDS42 DNA NC_ Escherichia coli str. K-12 substr. DH10B NC_ Escherichia coli str. 'clone D i2' NC_ PF0776 NC_ La111 NC_ N53-1 NC_ J1-220 Mycobacterium Tuberculosis Cluster NC_ RGTB327 NC_ RGTB423

19 NC_ NC_ NC_ NC_ Accession number NC_ NC_ NC_ NC_ NC_ str. Beijing/NITR203 str. Haarlem/NITR202 CAS/NITR204 EAI5/NITR206 Pseudomonas aeruginosa Strain Name Pseudomonas aeruginosa c7447m Pseudomonas aeruginosa PA1R Pseudomonas aeruginosa PAO1-VE13 Pseudomonas aeruginosa PAO1-VE2 Pseudomonas aeruginosa PAO581

20 Table S3. Summary of recombination analyses by PHIpack software for 14 analyzed species Species a Number of tested genes Recombinant genes (%) Nonrecombinant genes (%) Noninformative genes (%) B. cereus C. jejuni C. botulinum C. diphteriae C. pseudotuberculosis* E. coli-shigella F. tularensis* H. influenzae L. monocytogenes MTBC* N. meningitidis P. aeruginosa S. pneumoniae Y. pestis* a Clonal species are marked with an asterisk

21 Table S4. Summary of pangene frequencies within the protein pangenomes based on the NCBI annotations of the 14 studied species (prior to HGT correction) Species a Pangenome size b Rare pangenes c Near Core pangenes d Core pangenes e B.cereus C. jejuni C. botulinum C. diphtheriae C.pseudotuberculosis* E. coli-shigella F. tularensis* H. influenzae L. monocytogenes MTBC* N. meningitidis P. aeruginosa S. pneumoniae Y. pestis* a Clonal species are marked with an asterisk b Number of pangenes (orthologous gene clusters) within pangenome c % of pangenes that are found in less than 25% of strains of a species d % of pangenes that are found in over 75% of strains of a species, but are not found in all strains e % of pangenes found in all strains of a species

22 Table S5. Correlations between aaai a and Percentage of genes lost b in the different bacterial species Species c Number of genomes Spearman Rho P-value B.cereus C. jejuni C. botulinum C. diphtheriae C.pseudotuberculosis* E. coli-shigella F. tularensis* H. influenzae L. monocytogenes MTBC* N. meningitidis P. aeruginosa S. pneumoniae Y. pestis* a Denotes for each strain within each species the average AAI for its pairwise comparisons to all other strains within that species b For each strain we calculated the percentage of genes that were clearly lost from that genome as 100*L/T, where L is the number of near core core pangenes that are absent from the genome and T is the total number of genes present within that genome, that were used to construct the species pangenome c Clonal species are marked with an asterisk

23 Table S6. Summary of pangene frequencies within the RAST annotated, length-corrected protein pangenomes of the 14 studied species Species a Pangenome size b Rare pangenes c Near Core pangenes d Core pangenes e B.cereus C. jejuni C. botulinum C. diphtheriae C.pseudotuberculosis* E. coli-shigella F. tularensis* H. influenzae L. monocytogenes MTBC* N. meningitidis P. aeruginosa S. pneumoniae Y. pestis* a Clonal species are marked with an asterisk b Number of pangenes (orthologous gene clusters) within pangenome c % of pangenes that are found in less than 25% of strains of a species d % of pangenes that are found in over 75% of strains of a species, but are not found in all strains e % of pangenes found in all strains of a species

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