Background
Methods
Bacterial culture and genomic DNA extraction
PacBio and Illumina MiSeq genome sequencing
Genome assembly and annotation
Processing of PacBio methylome data
Phylogenetic analysis
Quality assurance
Results and discussion
Strain metadata and genomic characteristics
Virulence factors | HP14039 | HP01234 | HP07036 | HP08058 | HP08061 | HP08074 | HP11049 | HP13005 | HP13050 | HP13068 | HP15005 | HP98490 | HP99255 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
cag-PAI |
–
|
–
| + |
–
| + |
–
|
–
| +a |
–
| + |
–
| + |
–
|
vacA
| + | + | + | + | + | + | + | + | + | + | + | + | + |
dupA
| + | + |
–
|
–
|
–
| +b |
–
|
–
|
–
|
–
|
–
|
–
|
–
|
iceA
| + | + | + |
–
|
–
| + | + | + |
–
| + | + | + | + |
babA
| + | + | + | + |
–
| +b | + | +b | +b | +b |
–
| + |
–
|
babB
| + |
–
| + | + | +b | +b |
–
|
–
|
–
| +b | + |
–
|
–
|
babC
|
–
| + |
–
|
–
| +b |
–
|
–
|
–
|
–
|
–
|
–
|
–
| + |
sabA
| + | + | + | + | + | + | + | + | + | + | + | + | + |
oipA
| + | + | + | + | + | + | + | + | + | + | + | + | + |
alpA
| + | + | + | + | + | + | + | + | + | + | + | + | + |
alpB
| + | + | + | + | + | + | + | + | + | + | + | + | + |
hopZ
| + | + | + | + | + | + | + | + | + | + | + | + | + |
napA
| + | + | + | + | + | + | + | + | + | + | + | + | + |
tieA/hp0986
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
ctkA/jhp0940
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
Methylome of HP14039
Recognition sitea | Modification type | No. detected | No. in genome | Detected (%) | Restriction component(s) | Methylation component(s) | Refs | ||||
---|---|---|---|---|---|---|---|---|---|---|---|
Locus tag | Ortholog | % identity | Locus tag | Ortholog | % identity | ||||||
5′-ACNGT | m4c | 976 | 1112 | 87.8 | HP14039_01407-01406 | K747_11000 | 94.1, 93.9 | HP14039_01408 | K747_10995 | 95.5 | [8] |
5′-ATTAAT | m6a | 949 | 952 | 99.7 | HP14039_01410 | jhp0431 | 94.1 | HP14039_01411 | jhp0430 | 94.9 | |
5′-CATG | m6a | 14,872 | 14,874 | 100 | HP14039_00716 | hp1209 | 93.3 | HP14039_00717 | hp1208 | 93.8 | [29] |
5′-CCATC | m6a | 2190 | 2199 | 99.6 | HP14039_00375-00376 | K747_12645 | 95.7, 92.7 | HP14039_00372-00373 | K747_03690 | 96.2, 97.7 | [8] |
5′-CCGG | m4c | 3535 | 3542 | 99.8 | HP14039_01604 | hp0262 | 96.1 | HP14039_01603 | hp0263 | 94.2 | [29] |
5′-CTNAG | m4c | 6164 | 6172 | 99.9 | HP14039_01555 | HpyHI | 96 | HP14039_01554 | M.HpyHI | 94.9 | [30] |
5′-GAGG | m6a | 4672 | 4718 | 99 | HP14039_00203b | – | – | HP14039_00204 | hp0050 | 95.2 | |
5′-GATC | m6a | 10,541 | 10,548 | 99.9 | HP14039_00158 | hp0091 | 93.7 | HP14039_00157 | hp0092 | 92.8 | [29] |
5′-GTAC | m6a | 300 | 304 | 98.7 | HP14039_01382-01381 | jhp0455 | 93.4, 93.7 | HP14039_01383 | jhp0454 | 95.8 | |
5′-GTNNAC | m6a | 820 | 826 | 99.3 | HP14039_00987 | hp0909 | 91.7 | HP14039_00986 | hp0910 | 96.1 | [29] |
5′-TCGA | m6a | 610 | 612 | 99.7 | – | – | – | HP14039_01606-01607 | hp0260 | 96.1, 97.6 | [32] |
5′-TCNNGA | m6a | 3795 | 3808 | 99.7 | HP14039_00847-00846 | jhp1013c | 96.8, 97.5 | HP14039_00848 | jhp1012 | 96.1 | [26] |
5′-TGCA | m6a | 11,060 | 11,072 | 99.9 | HP14039_00305 | HpyCH4 V | 96.6 | HP14039_00306 | M.HpyCH4 V | 93.4 | |
5′-CTANNNNNNNTAYG | m6a | 191 | 192 | 99.5 | – | – | – | HP14039_00325d | K747_03505 | 93 | [8] |
5′-WCANHNNNNTG | m6a | 1732 | 4440 | 39 | – | – | – | HP14039_01429e | K747_10905 | 92 | [8] |