Oligonucleotide array sequencing of T.pallidum ssp. pallidum
strain SS14.

D 2006

Oligonucleotide array sequencing of T.pallidum ssp. pallidum strain SS14.

MATĚJKOVÁ, Petra, Michal STROUHAL, David ŠMAJS, J.K. HOWELL, S.J. NORRIS et. al.

Základní údaje

Originální název

Oligonucleotide array sequencing of T.pallidum ssp. pallidum strain SS14.

Název česky

Oligonukleotidové čipy - sekvenace T.pallidum ssp. pallidum SS14.

Autoři

MATĚJKOVÁ, Petra, Michal STROUHAL, David ŠMAJS, J.K. HOWELL, S.J. NORRIS, T.J. ALBERT a G.M. WEINSTOCK

Vydání

Barga, Italy, Gordon Research Conference 2006, Biology of Spirochetes. 1 s. 2006

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

Genetika a molekulární biologie

Stát vydavatele

Itálie

Utajení

není předmětem státního či obchodního tajemství

Organizační jednotka

Lékařská fakulta

Klíčová slova česky

CGS, Treponema pallidum, kmen SS14, sekvencování na čipu

Klíčová slova anglicky

CGS, Treponema pallidum, strain SS14, array sequencing

Změněno: 26. 6. 2009 16:41, prof. MUDr. David Šmajs, Ph.D.

Anotace

ORIG CZ

V originále

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.

Česky

Pro sekvenaci bakterie Treponema pallidum ssp. pallidum kmene SS14 byla použita strategie komparativního genomického sekvencování. Celkem bylo nalezeno 317 SNPs, 10 delecí a 9 inzercí. Sekvenační strategie na čipech představuje rychlou, levnou a dostupnou metodu pro sekvenaci blízce příbuzných genomů.

Návaznosti

GA310/04/0021, projekt VaV

Název: Postgenomické studie syfilitické spirochety Treponema pallidum

Investor: Grantová agentura ČR, Postgenomické studie syfilitické spirochety Treponema pallidum

Citovat

MATĚJKOVÁ, Petra, Michal STROUHAL, David ŠMAJS, J.K. HOWELL, S.J. NORRIS, T.J. ALBERT a G.M. WEINSTOCK. Oligonucleotide array sequencing of T.pallidum ssp. pallidum strain SS14. In Gordon Research Conference 2006, Biology of Spirochetes. Barga, Italy, 2006, 1 s.

@inproceedings{704256,
   author = {Matějková, Petra and Strouhal, Michal and Šmajs, David and Howell, J.K. and Norris, S.J. and Albert, T.J. and Weinstock, G.M.},
   address = {Barga, Italy},
   booktitle = {Gordon Research Conference 2006, Biology of Spirochetes.},
   keywords = {CGS, Treponema pallidum, strain SS14, array sequencing},
   language = {eng},
   location = {Barga, Italy},
   title = {Oligonucleotide array sequencing of T.pallidum ssp. pallidum strain SS14.},
   year = {2006}
}

TY  - JOUR
ID  - 704256
AU  - Matějková, Petra - Strouhal, Michal - Šmajs, David - Howell, J.K. - Norris, S.J. - Albert, T.J. - Weinstock, G.M.
PY  - 2006
TI  - Oligonucleotide array sequencing of T.pallidum ssp. pallidum strain SS14.
CY  - Barga, Italy
KW  - CGS, Treponema pallidum, strain SS14, array sequencing
N2  - 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.
ER  -

MATĚJKOVÁ, Petra, Michal STROUHAL, David ŠMAJS, J.K. HOWELL, S.J. NORRIS, T.J. ALBERT a G.M. WEINSTOCK. Oligonucleotide array sequencing of T.pallidum ssp. pallidum strain SS14. In \textit{Gordon Research Conference 2006, Biology of Spirochetes.}. Barga, Italy, 2006, 1 s.

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