Oligonucleotide array sequencing of T.pallidum ssp. pallidum strain SS14.
| Authors | |
|---|---|
| Year of publication | 2006 |
| Type | Article in Proceedings |
| Conference | Gordon Research Conference 2006, Biology of Spirochetes. |
| MU Faculty or unit | |
| Citation | |
| Field | Genetics and molecular biology |
| Keywords | CGS, Treponema pallidum, strain SS14, array sequencing |
| Description | Comparative genomic sequencing strategy (CGS) was employed to sequence the bacterium Treponema pallidum ssp. pallidum strain SS14. Hybridization to a dense oligonucleotide tiling array based on sequence of Treponema pallidum ssp. pallidum strain Nichols discovered regions of different sequence in SS14 and sequencing array designed to reveal single nucleotide changes in combination with dideoxy-terminator sequencing of hypervariable regions was used to complete genome sequence of SS14 strain. Altogether 317 SNPs, 10 deletions and 9 insertions were found. 301 SNPs, 9 deletions and 6 insertions represented changes in coding sequences and lead to 4 frameshifts, 1 nonsense mutation, 1 read through stop codon mutation, 35 conservative aa changes and 177 non-conservative aa changes. 35.5 kb of randomly chosen regions were sequenced to verify the CGS output resulting in error rate 4 x 10-4. 63% SNPs affected hypothetical genes and protein analysis showed that 66% of all amino acid were in proteins with unknown function. Our confirmation experiments identified phase variation in T. pallidum population and suggested potential for identifying of these loci by CGS. Array sequencing strategy represents a rapid, cost effective and scalable method for sequencing of closely related genomes. |
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