SUPPLEMENTARY TABLES Table S1 Gene Primer Sequence Position (Size)

Transcription

1 SUPPLEMENTARY TABLES Table S1 Primers used for gdna and mrna analyses Gene Primer Sequence Position (Size) mga F: 5 -TGGTTATATTACAATCTGGTACCATC (208) R: 5 -GGTATGCGTCAAATAGGCATTGG emm23 F: 5'-GCTTTGACAGTTTTAGGGACAGG (331) R: 5'-GTGCTCCATCAAGCGTTGTATTC scpa F: 5 -GCAGGCAAAGGAGCTGGGACT (307) R: 5 -GCATCGCACCTTCTAGGCGGT sfb1 F: 5 -GGCGATTTGCTGTCACTTTAGTGG (454) R: 5 -GGTTCTAAACCCTCCATGATTCCA fbp54 F: 5 -CGGTCATATCCAAAAGGTCAATC (344) R: 5 -CTGCACGGTCCACCAAGATGATA speb F: 5'-CAGCAGCTATCAAAGCAGGTGCAC (284) R: 5'-CTCAGCGGTACCAGCATAAGTAG spd3 F: 5'-ACAAGTACTGTTACGGCAGCCAG (307) R: 5'-GGTAACCAACTAAATGGCCACGG hasa F: 5 -GAGCCATTTAAAGGAAATCCACATG (295) R: 5'-CGTCAGCGTCAGATCTTTCAAATGC sk F: 5 -GGAACAGTCAAGCCTGTCCAAGCT (209) R: 5 -GGTTTTGATTTTGGACTTAAGCC slo F: 5 -GCTAGTACAGAAACCACAACGAC (409) R: 5 -GATAGGTCCTATCAGTGACAGAGTC spd F: 5'-GGCTGTAACAACAGTCACACTTG (294) R: 5'-GATTGTCTAACACCGTAGCTACC plr (gaphdh) F: 5 -GACGGTACTGAAACAGTTATCTC (234) R: 5 -GATAGCTTTAGCAGCACCAGTTG a The positions of the primers are relative to the A 1 TG of the particular gene. The size of the amplicon for each gene is also listed in parentheses.

2 Gene TABLE S2 Known virulence genes encoded by phage and chromosomes in 21 sequenced GAS strains a A20 SF370 M M3 315 M3 SSI-1 M M5 Manfredo a +/- represents the presence/absence of the specified gene in each strain. M Phage sda slaa spd spd spea spec speh spei spek spel spem ssa Chromosomal cfa dlta dltc endos eno grab hasa hyla ides lbp nga plr prts saga scla scpa sfb sic sk slo smez speb spd speg spej spya

3 Gene TABLE S2 (cont'd) Known virulence genes encoded by phage and chromosomes in 21 sequenced GAS strains a HKU16 4 HSC M23ND M28 N6180 M49 NZ131 M53 Alab49 Phage sda slaa spd spd spea spec speh spei spek spel spem ssa Chromosomal cfa dlta dltc endos eno grab hasa hyla ides lbp nga plr prts saga scla scpa sfb sic sk slo smez speb spd speg spej spya a +/- represents the presence/absence of the specified gene in each strain. M M

4 Supplementary Figures FIG S1 FIG S1 Genome comparisons of fully sequenced S. pyogenes strains. (A-D) Pair-wise genome comparison of the 21 fully-sequenced GAS strains derived from the NCBI database. The four subfigures (A-D) can be concatenated. The red and blue lines represent forward and reverse alignments, respectively. The genomes of the first 17 strains are highly syntenic, except for small gaps induced by prophages and short mobile elements. The genomes of the last four strains, M23ND, M5 Manfredo, 2 HKU16, and M3 SSI-1, exhibit complex rearrangements, including inversions and translocations. An extra short inversion within the last 100 kb of the chromosome occurred specifically in the genome of S. pyogenes M23ND.

5 FIG S2 FIG S2 Phylogenetic relationships among the fully sequenced S. pyogenes genomes. The sequences of the 20 previously sequenced GAS genomes were obtained from the NCBI database and compared using using SplitsTree. (A) Phylogenetic trees were based on pair-wise distances from whole genome comparisons and constructed using BLAST tree method of Fast Minimum Evolution. (B) The phylogenetic network was based on MLST of seven commonly used housekeeping genes (gki, gtr, muri, muts, recp, xpt, yqil) using SplitDecomposition for network construction and uncorrected p-distance for distance estimation. The phylogenetic relationships represented by the network were concordant with the tree diagram from whole-genome comparison (A). It showed that M23ND shares the common ancestor, , with M5 Manfredo and M , but experienced a distinct evolutionary path. (C) Phylogenetic network based on SNP profiling of chromosomally-inherited virulence genes, excluding the divergent genes, sfb1, sic, grab, endos, ides, and ska using NeighborNet for network construction and uncorrected p-distance for distance estimation. The network was topologically similar to the primary evolutionary structure inferred from the pair-wise whole-genome comparisons (A) and the MLST of seven housekeeping genes (B). M23ND is most closely related to strains M5 Manfredo and M , and they may also share a common ancestor with , which diverged more recently.

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