Comparison of 61 E. coli genomes

Transcription

1 Comparison of 61 E. coli genomes Center for Biological Sequence Analysis Department of Systems Biology Dave Ussery! DTU course Comparative Genomics Oksana s 61 E. coli genomes paper! Monday, 23 June, 2014

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3 Microb Ecol DOI /s MINIREVIEWS Comparison of 61 Sequenced Escherichia coli Genomes Oksana Lukjancenko & Trudy M. Wassenaar & David W. Ussery Note: Include title slide with names of the group, title of the project 23 June,

4 Abstract Escherichia coli is an important component of the biosphere and is an ideal model for studies of processes involved in bacterial genome evolution. Sixty-one publically available E. coli and Shigella spp. sequenced genomes are compared, using basic methods to produce phylogenetic and proteomics trees, and to identify the pan- and core genomes of this set of sequenced strains. A hierarchical clustering of variable genes allowed clear separation of the strains into clusters, including known pathotypes; clinically relevant serotypes can also be resolved in this way. In contrast, when in silico MLST was performed, many of the various strains appear jumbled and less well resolved. The predicted pan-genome comprises 15,741 gene families, and only 993 (6%) of the families are represented in every genome, comprising the core genome. The variable or accessory genes thus make up more than 90% of the pan-genome and about 80% of a typical genome; some of these variable genes tend to be co-localized on genomic islands. The diversity within the species E. coli, andthe overlap in gene content between this and related species, suggests a continuum rather than sharp species borders in this group of Enterobacteriaceae. 23 June,

5 O. Lukjancenko et al. Figure 1 Phylogenetic tree based on extracted 16S rrna sequences. a Comparison of 20 different Enterobacteriaceae, based on extracted 16S rrna sequences from the GenBank sequence files. E. coli and Shigella are shown in green. b Tree of 61 sequenced E. coli (black) andrelatedspecies (colored), based on the alignment of the 16S rrna gene sequence. Apart from Shigella spp., the genes from E. albertii and E. fergusonii are also included (arrows). The 16S rrna gene of S. enterica Typhimurium LT2 was used as the root. Bootstrap values, indicated in red, show that most nodes are predicted with uncertainty; nevertheless, the genera Escherichia spp. and Shigella spp. are not separated in this tree, and the three Escherichia species are also mixed a Enterobacteriaceae genera 16S rrna tree Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis Yersinia pestis Angola Proteus mirabilis HI4320 Xenorhabdus bovienii SS-2004 Photorhabdus asymbiotica ATCC Edwardsiella ictaluri Dickeya dadantii Ech586 Serratia proteamaculans 568 Pectobacterium atrosepticum SCRI The Big Picture 16S rrna tree Klebsiella pneumoniae 342 Eneterobacter species Erwinia amylovora ATCC Citrobacter sakazakii ATCC BAA Salmonella enterica serovar Typhimurium LT2 954 Citrobacter koseri ATCC BAA Shigella boydii CDC Escherichia coli K-12 MG1655 Q: How does E. coli relate? Sodalis glossinidius 'morsitans' Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum) Buchnera aphidicola str 5A (Acyrthosiphon pisum) 23 June,

6 2. Delve into details - first results.. b Question: Why is there poor resolution between E. coli genomes? 343 E. coli S. dysenteriae Sd197 E. coli CFT073 E. coli E22 E. coli O103:H2 str E. coli B str. REL606 E. coli BL21 (DE3) E. coli BL21 (DE3) S. sonnei Ss046 E. coli E. coli E E. coli 536 S. flexneri 5 str S. flexneri 2a str. 2457T S. boydii Sb S. flexneri 2a str. 301 S. boydii CDC E. coli O26:H11 str E. coli B7A 790 E. albertii TW E. coli BL21 (DE3) E. coli APEC O E. fergusonii ATCC35469 E. coli UTI89 E. coli SE15 E. coli O127:H6 str. E2348/69 S. dysenteriae E. coli S E. coli ED1a E. coli Oslo O103 E. coli F11 E. coli IAI E. coli HS E. coli K12 str. ATCC E. coli O111:H- str E. coli E24377A 404 E. coli K12 str. BW2952 E. coli E. coli IAI1 E. coli O157:H7 str. EC4042 E. coli O157:H7 str. EC4045 E. coli O157:H7 str. EC4076 E. coli O157:H7 str. EC4113 E. coli O157:H7 str. EC4115 E. coli O157:H7 str. EC4196 E. coli O157:H7 str. EC4401 E. coli O157:H7 str. Sakai E. coli O157:H7 str. TW14588 E. coli SMS-3-5 E. coli SE11 E. coli UMN E. coli K12 str. DH1 16S rrna tree S. enterica Typhimurium str. LT2 E. coli O157:H7 str. EDL933 E. coli O157:H7 str. EC E. coli O157:H7 str. EC4501 E. coli O157:H7 str. EC4486 E. coli O157:H7 str. EC4206 E. coli O157:H7 str. LANL ECF 225 E. coli O157:H7 str. EC508 E. coli O157:H7 str. LANL ECA E. coli K12 str. W E. coli K12 str. MG1655 E. coli K12 str. DH10B June,

7 pan-genome family tree Relati ve manhattan distance E. coli O157:H7 str. EC4196 E. coli O157:H7 str. EC4113 E. coli O157:H7 str. EC508 E. coli O157:H7 str. EC4501 E. coli O157:H7 str. EC4076 E. coli O157:H7 str. EC4115 E. coli O157:H7 str. EC4042 E. coli O157:H7 str. EC4486 E. coli O157:H7 str. EC869 E. coli O157:H7 str. EC4206 E. coli O157:H7 str. EC4401 E. coli O157:H7 str. EDL933 E. coli O157:H7 str. Sakai E. coli O157:H7 str. TW14588 E. coli O157:H7 str. LANL ECF E. coli O157:H7 str. LANL ECA E. coli O157:H7 str. EC4045 E. coli K12 str. W3110 E. coli K12 str. MG1655 E. coli K12 str. DH1 E. coli K12 str. BW2952 E. coli K12 DH10B E. coli K12ATCC8739 E. coli B str. REL606 E. coli BL21 (DE3Korea) E. coli BL21 (DE3 AU) E. coli BL21 (DE3 DOE) E. coli HS E. coli SE11 E. coli IAI1 E. coli E. coli E24377A E. coli O26:H11 str E. coli O103:H2 str E. coli O111:H str E. coli O103 Oslo E. coli SMS 3 5 E. coli UMN026 E. coli E. coli IAI39 E. coli UTI89 E. coli S88 E. coli CFT073 E. coli SE15 E. coli 536 E. coli O127:H6 str. E2348/69 E. coli ED1a E. coli F11 E. coli APECO1 E. coli E E. coli E22 E. coli B7A E. coli S. boydii CDC S. boydii Sb227 S. sonnei Ss046 S. flexneri 2a str. 2457T S. flexneri 2a str. 301 S. flexneri 5 str Salmonella enterica Typhimurium str. LT2 E. fergusonii ATCC E. albertii TW07627 S. dysenteriae 1012 S. dysenteriae Sd Figure 3 Pan-genome clustering of E. coli (black) and related species (colored), based on the alignment of their variable gene content. The genomes now cluster according to species and a relatedness between E. coli K12 derivatives (green block) and group B isolates (orange block) is visible Question: Does the grouping of the E. coli genomes make sense? 23 June,

8 pan- / core-genome plot O. Lukjancenko et al. Number of gene families Core genome Pan genome New gene families : Escherichia coli 0157:H7 str. EC : Escherichia coli 0157:H7 str. EC : Escherichia coli 0157:H7 str. EC508 4 : Escherichia coli 0157:H7 str. EC : Escherichia coli 0157:H7 str. EC : Escherichia coli 0157:H7 str. EC : Escherichia coli 0157:H7 str. EC : Escherichia coli 0157:H7 str. EC : Escherichia coli 0157:H7 str. EC : Escherichia coli 0157:H7 str. EC : Escherichia coli 0157:H7 str. EC : Escherichia coli 0157:H7 str. EDL : Escherichia coli 0157:H7 str. TW : Escherichia coli 0157:H7 str. Sakai 15 : Escherichia coli 0157:H7 EC : Escherichia coli 0157:H7 str. LANL ECF 17 : Escherichia coli 0157:H7 str. LANL ECA 18 : Escherichia coli K12 str. DH10B 19 : Escherichia coli K12 str. MG : Escherichia coli K12 str. W : Escherichia coli K12 str. DH1 22 : Escherichia coli BW : Escherichia coli ATCC : Escherichia coli B REL : Escherichia coli BL21 (DE3 Korea) 26 : Escherichia coli BL21 (DE3 AU) 27 : Escherichia coli BL21 (DE3 DOE) 28 : Escherichia coli HS 29 : Escherichia coli SE11 30 : Escherichia coli IAI1 31 : Escherichia coli : Escherichia coli E24377A 33 : Escherichia coli O26:H11 str : Escherichia coli 0127:H6 str. E2348/69 35 : Escherichia coli O103:H2 str : Escherichia coli O111:H- str : Escherichia coli 0103 Oslo 38 : Escherichia coli SMS : Escherichia coli UMN : Escherichia coli : Escherichia coli IAI39 42 : Escherichia coli UTI89 43 : Escherichia coli S88 44 : Escherichia coli CFT : Escherichia coli SE15 46 : Escherichia coli : Escherichia coli ED1a 48 : Escherichia coli F11 49 : Escherichia coli APECO1 50 : Escherichia coli E : Escherichia coli E22 52 : Escherichia coli B7A 53 : Escherichia coli : Shigella flexneri 2a 2457T 55 : Shigella flexneri 2a : Shigella flexneri : Shigella boydii CDC : Shigella boydii Sb : Shigella sonnei Ss : Escherichia fergusonii ATCC : Escherichia albertii TW : Salmonella enterica Typhimurium LT2 63 : Shigella dysenteriae Sd : Shigella dysenteriae 1012 Figure 4 Pan- and core genome plot of the analyzed genomes. The blue pan-genome curve connects the cumulative number of gene families present in the analyzed genomes. The red core genome curve connects the conserved number of gene families. The gray bars show the numbers of novel gene families identified in each genome Question: What happened when E. coli genome #18 was added? 23 June,

9 MLST tree Figure 2 Phylogenetic tree of concatenated MLST gene alleles (adk, fumc, icd, gyrb, mdh, pura, reca), extracted from the genome sequences. Color use is the same as in Fig. 1 E. coli O157:H7 str. LANL ECA E. coli O157:H7 str. EC4113 E. coli O157:H7 str. TW14588 E. coli O157:H7 str. EC4196 E. coli O157:H7 str. EC869 E. coli O157:H7 str. EC4486 E. coli O157:H7 str. EC508 E. coli O157:H7 str. EC4042 E. coli O157:H7 str. LANL ECF E. coli O157:H7 str. EC4501 E. coli O157:H7 str. EDL933 E. coli O157:H7 str. EC4045 E. coli O157:H7 str. EC4076 E. coli O157:H7 str. EC4115 E. coli O157:H7 str. Sakai E. coli O157:H7 str. EC4206 E. coli O157:H7 str. EC4401 Shigella flexneri 2a str. 301 Shigella flexneri 5 str Shigella flexneri 2a str. 2457T Shigella dysenteriae Sd197 E. coli E24377A Shigella boydii Sb227 Shigella boydii CDC Shigella sonnei Ss E. coli E E. coli O26:H11 str E. coli O111:H- str E. coli SE11 E. coli B7A E. coli O103:H2 str E. coli E22 E. coli Oslo O103 E. coli E. coli IAI1 E. coli E. coli HS E. coli K12 str. ATCC 8739 E. coli UMN026 E. coli SMS-3-5 E. coli IAI39 E. coli SE15 E. coli O127:H6 str. E2348/69 E. coli ED1a E. coli CFT073 E. coli APEC O1 E. coli UTI89 E. coli S88 E. coli F11 E. coli 536 Shigella dysenteriae 1012 E. coli BW2952 E. coli K12 str. W E. coli K12 str. DH10B E. coli K12 str. DH1 830 E. coli K12 str. MG1655 E. coli E. coli B str. REL606 E. coli BL21(DE3) E. coli BL21(DE3) E. coli BL21(DE3) O. Lukjancenko et al. E. albertii TW07627 E. fergusonii ATCC354 Question: Why is there poor resolution between the O157 E. coli genomes? June,

10 Comparison of 61 Sequenced Escherichia coli Genomes BLAST atlas Figure 5 BLAST atlas. In the middle, a genome atlas of E. coli O157:H7 strain EC4115 is shown, around which BLAST lanes are shown. Every lane corresponds to a genome, with the following colors (going outwards): green E. coli O157: H7 (15 lanes); light blue E. coli LANL strains (two lanes); dark blue Shigella spp. (eight lanes); red E. coli K12 and derivatives (six lanes); orange E. coli strain Bphylogroup(fourlanes); followed by all other E. coli genomes in different colors. The outermost three lanes represent E. fergusonii, E. albertii, ands. enterica Typhimurium LT2. Lack of color indicates that the genes at that position in strain EC4115 were not found in the genome of that lane. The position of replication origin and terminus is indicated Origin 4M 4.5M 3.5M 5M 3M 0M 2.5M 0.5M Escherichia coli O157:H7 strain EC4115 2M 1M 1.5M Terminus Question: What is the cluster of highly conserved E. coli genes unique to O157? 23 June,

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