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| Status |
Public on Oct 04, 2012 |
| Title |
The Methylomes of Six Bacteria |
| Organisms |
Campylobacter jejuni; Bacillus cereus; Geobacter metallireducens; Chromohalobacter israelensis; Vibrio breoganii |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens, Vibrio breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81-176 and Campylobacter jejuni NCTC 11168, all of which had previously been sequenced using other platforms were re-sequenced using single-molecule, real-time (SMRT) sequencing specifically to analyze their methylomes. In every case a number of new N6-methyladenine (m6A) and N4-methylcytosine (m4C) methylation patterns were discovered and the DNA methyltransferases (MTases) responsible for those methylation patterns were assigned. In 15 cases it was possible to match MTase genes with MTase recognition sequences without further sub-cloning. Two Type I restriction systems required sub-cloning to differentiate their recognition sequences, while four MTases genes that were not expressed in the native organism were sub-cloned to test for viability and recognition sequences. No attempt was made to detect 5-methylcytosine (m5C) recognition motifs from the SMRT sequencing data because this modification produces weaker signals using current methods. However, all predicted m6A and m4C MTases were detected unambiguously. This study shows that the addition of SMRT sequencing to traditional sequencing approaches gives a wealth of useful functional information about a genome showing not only which MTase genes are active, but also revealing their recognition sequences.
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| Overall design |
Examination of the methylomes of six different strains of bacteria using kinetic data from single-molecule, real-time (SMRT) sequencing on the PacBio RS.
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| Contributor(s) |
Murray IA, Clark TA, Morgan RD, Boitano M, Anton BP, Luong K, Fomenkov A, Turner SW, Korlach J, Roberts RJ |
| Citation(s) |
23034806 |
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| Submission date |
Aug 15, 2012 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Tyson A Clark |
| E-mail(s) |
[email protected]
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| Phone |
650-521-8319
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| Organization name |
Pacific Biosciences
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| Street address |
1380 Willow Rd.
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| City |
Menlo Park |
| State/province |
CA |
| ZIP/Postal code |
94025 |
| Country |
USA |
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| Platforms (5)
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| GPL15935 |
PacBio RS (Geobacter metallireducens) |
| GPL15936 |
PacBio RS (Chromohalobacter salexigens) |
| GPL15937 |
PacBio RS (Vibrio breoganii) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA172894 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40133_RAW.tar |
2.2 Gb |
(http)(custom) |
TAR (of CSV, GFF) |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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