Supplementary material

Unexpected diversity in the mobilome of a Pseudomonas aeruginosa strain isolated from a

dental unit waterline revealed by SMRT Sequencing

Antony T. Vincent1,2,3, Steve J. Charette*1,2,3 and Jean Barbeau4

1. Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, Canada

2. Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec

(CRIUCPQ), Quebec City, Canada

3. Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec

City, Canada

4. Département de stomatologie, Faculté de Médecine Dentaire, Université de Montréal,

Montreal City, Canada

*Steve J. Charette, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-

Eugène-Marchand, 1030 avenue de la Médecine, Université Laval, Quebec City, QC, Canada,

G1V 0A6. E-mail: Steve.Charette@bcm.ulaval.ca

Table S1. Detailed information on the insertion sequences found in the genome of PPF-1Copy Strand Coordinate Status Interrupted genes/products Best hita Identitya Score (bits)a

ISPa11

1 -1708755..1709852 Complete IS1394 716/828 753

2 +1954326..1955423 Complete Ankyrin repeat protein IS1394 716/828 753

3 +2094291..2095388 Complete wzx IS1394 716/828 753

4 -2096061..2097158 Complete wzx IS1394 716/828 753

5 +3151107..3152204 Complete IS1394 716/828 753

6 +3474181..3475278 Complete Hypothetical protein IS1394 716/828 753

7 +4306277..4307374 Complete Putative membrane protein IS1394 716/828 753

8 -4388713..4389810 Complete lasR IS1394 716/828 753

9 -4708799..4709896 Complete Hypothetical protein IS1394 716/828 753

10 -4900825..4901922 Complete ABC transporter permease IS1394 716/828 753

11 -4902319..4903416 Complete IS1394 716/828 753

12 -6332622..6333719 Complete sel1 repeat family protein IS1394 716/828 753

IS2221 + 65040..65121 Partial IS222 80/82 147

2 +2538331..2539566 Complete IS222 1209/1236 2236

3 -2680814..2681582 Partial IS222 740/766 1312

4 -2983015..2984250 Complete Fimbrial protein IS222 1208/1236 2228

5 +5102312..5103547 Complete HNH endonuclease ? IS222 1208/1236 2228

ISPa16

1 -2656803..2657994 Complete Putative phage integrase ? ISPa16 1191/1192 2355

ISPa32

1 +5089489..5090725 Complete Site-specific integrase ? ISPa32 1217/1237 2286

ISPa37

1 -2679361..2680813 Complete IS222 ? ISPa37 1447/1453 2833

ISPpu1

1 +1575777..1576940 Complete Putative integrase ? ISPpu1 1164/1164 2307

ISPst121 + 289160..290490 Complete ISPst3 ? ISPst12 1327/1331 2607

ISPst31 + 290478..291259 Partial nrdJb ? ISPst3 756/770 1407

a: Results of blastn analyzes done on ISfinder database (Siguier et al. 2006)

Table S2. Identity of group II introns found in the genome of PPF-1 with those available in GenBank (identified with MegaBLAST)

IntronStrain (accession number) P.ae.I2 P.ae.I4 P.ae.I3 P.ae.I5

Pa58 (CP021775.1) 2847/28472944/2990 1850/1850

W45909 (CP008871.2) 2846/28472930/2991 1850/1850

RIVM−EMC2982 (CP016955.1) 2846/28472965/2991 1850/1850

FA−HZ1 (CP017353.1) 2846/28472929/2991 1850/1850

Carb01 63 (CP011317.1) 2846/28472965/2991 1850/1850

FRD1 (CP010555.1) 2846/28472964/2991 1850/1850

PA38182 (HG530068.1) 2846/28472963/2991 1850/1850

Pa1242 (CP022002.1) 2839/28472963/2991 1850/1850

M1608 (CP008862.2) 2847/28472930/2991 2417/2418

M37351 (CP008863.1) 2847/28472930/2991 2418/2418

BAMCPA07−48 (CP015377.1) 2846/28472930/2991

H47921 (CP008861.1) 2845/28472989/2991

W16407 (CP008869.2) 2845/28472965/2991

L10 (CP019338.1) 2847/2847T38079 (CP008866.2) 2847/2847S86968 (CP008865.2) 2847/2847PA14Or_reads (LT608330.1) 2847/2847S04 90 (CP011369.1) 2847/2847UCBPP−PA14 (CP000438.1) 2847/2847PA83 (CP017293.1) 2845/2847F9670 (CP008873.1) 2845/2847

W60856 (CP008864.2)2967/2990

H27930 (CP008860.2)2896/2991

PASGNDM699 (CP020704.1) 1850/1850PASGNDM345 (CP020703.1) 1850/1850F63912 (CP008858.2) 1850/1850B10W (CP017969.1) 1850/1850

DHS01 (CP013993.1) 1850/18508380 (AP014839.2) 1850/1850F22031 (CP007399.1) 1850/1850SCV20265 (CP006931.1) 1850/1850PSE9 (PAGI−7 GEI) (EF611303.1) 1850/1850DK2 (CP003149.1) 2418/2418

Figure S1. Distribution of 562 genes associated to genomic islands into functional categories.

Figure S2. Molecular phylogeny of 317 intron-encoded proteins (IEPs) as described in the main text. Classes [Bacterial A, B, C, D, E, F and G, mitochondrial-like (ML), and chloroplast-like (CL1 and CL2)] of introns are annotated according to the Database for bacterial group II introns (Candales et al. 2012). The four introns found in the P. aeruginosa strain PPF-1 (P.ae.I2, P.ae.I3, P.ae.I4 and P.ae.I5) are indicated by black arrows.

REFERENCES

Candales, M. A., Duong, A., Hood, K. S., Li, T., Neufeld, R. A. E., Sun, R. et al. 2012. Database for bacterial group II introns. Nucleic Acids Res. 40: D187–D190. doi:10.1093/nar/gkr1043

Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. 2006. ISfinder: the reference centrefor bacterial insertion sequences. Nucleic Acids Res. 34: D32–D36. doi:10.1093/nar/gkj014.