Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements

Table 2 Modular composition and properties of defined tfs4 ICE types in reference strains

						Annotated genes contained within particular variant L-C-R modules^a
Strain^b	ICEHp type^c	ICE type (L-C-R)^d	No. intact^e	ICE size^f (bp)	Position in genome	L1/L2/Lm	C1/C2	R1/R2/R1f
G27	tfs4b	L1C1R1	37	39,129	1,045,701-1,085,076	986-981	980-966	965-959
Shi470	tfs4b	L1C1R1	37	39,376	874,706-913,876	4480-4505	4510-4595	4600-4640
R036d	–	L2C2R2	9	39,125	403,599-442723^g	1010-1000	999-985	984-976
P12	tfs4a	L2C1R2	2	40,644	452,130-492,773	437-446	447-463	464-473
NQ4053	–	L2C1R1	2	40,414	338,351-378764^h	1511-1502	1501-1476	1590-1596
P-25	–	L2C1R1f	34	35,201	685,842-721042ⁱ	1438-1425	1424-1406	1405-1401
A-8	–	L1C1R1f	3	35,548	275,596-311143^j	945-939	938-919	917-913
A-11	–	LmC1R1	2	38,543	689,499-728042^k	756-748	747-729	728-721
PeCan4	tfs4a	LmC1R2	1	40,987	1,537,078-1,578,064	7835-7800	7785-7710	7705-7670
SAfrica7	tfs4c	LmC2R2	1	41,220	1,527,377-1,568,596	7710-7670	7665-7595	7590-7540

^aAutomated gene numbering increases in multiples of either 1 or 5 (strains Shi470, PeCan4 and SouthAfrica7) in the Genbank annotation of the selected genome sequences
^bRepresentative reference strains harbouring different defined tfs4 ICE types (with the exception of G27/Shi470) for which contiguous ICE sequences are available
^cAs defined in [44]
^dL-C-R refers to particular types of left (L1/L2/Lm), central (C1/C2) or right (R1/R2/R1f) tfs4 ICE modules comprising different subsets of orthologous genes
^eIntactness of different tfs4 ICE types in strains based on the relative representation of component modules
^fTotal length of tfs4 ICE sequences between left and right flanking xer excision motifs as defined in [42]
^gHpR036dcontig.3, accession: NZ_AMOT01000004.1
^hNQ4053contig.5_1, accession NZ_AKNV01000006.1
ⁱHpP_25.contig.1, accession AKPS01000002.1
^jHpA_8.contig.3_1, accession AKOS01000004.1
^kHpA_11.contig.0, accession NZ_AOTW01000001.1

ISSN: 1759-8753