Complete genome sequences of two strains of Treponema pallidum
subsp pertenue from Indonesia: Modular structure of several
treponemal genes

J 2018

Complete genome sequences of two strains of Treponema pallidum subsp pertenue from Indonesia: Modular structure of several treponemal genes

STROUHAL, Michal, Lenka PAŠTĚKOVÁ, Jan HAVIERNIK, Sascha KNAUF, Sylvia BRUISTEN et. al.

Základní údaje

Originální název

Complete genome sequences of two strains of Treponema pallidum subsp pertenue from Indonesia: Modular structure of several treponemal genes

Autoři

STROUHAL, Michal (203 Česká republika, domácí), Lenka PAŠTĚKOVÁ (203 Česká republika, domácí), Jan HAVIERNIK (203 Česká republika, domácí), Sascha KNAUF (276 Německo), Sylvia BRUISTEN (528 Nizozemské království), Gerda T. NOORDHOEK (528 Nizozemské království), Jan OPPELT (203 Česká republika, domácí), Darina ČEJKOVÁ (203 Česká republika) a David ŠMAJS (203 Česká republika, garant, domácí)

Vydání

PLoS neglected tropical diseases, San Francisco, Public Library of Science, 2018, 1935-2735

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

30309 Tropical medicine

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.487

Kód RIV

RIV/00216224:14110/18:00101497

Organizační jednotka

Lékařská fakulta

DOI

http://dx.doi.org/10.1371/journal.pntd.0006867

UT WoS

000449318100059

Klíčová slova anglicky

Treponema pallidum subsp. pertenue

Štítky

14110513, CF BIOIT, podil, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 30. 4. 2019 09:22, Soňa Böhmová

Anotace

V originále

Background Treponema pallidum subsp. pertenue (TPE) is the causative agent of yaws, a multistage disease endemic in tropical regions in Africa, Asia, Oceania, and South America. To date, seven TPE strains have been completely sequenced and analyzed including five TPE strains of human origin (CDC-2, CDC 2575, Gauthier, Ghana-051, and Samoa D) and two TPE strains isolated from the baboons (Fribourg-Blanc and LMNP-1). This study revealed the complete genome sequences of two TPE strains, Kampung Dalan K363 and Sei Geringging K403, isolated in 1990 from villages in the Pariaman region of Sumatra, Indonesia and compared these genome sequences with other known TPE genomes. Methodology/principal findings The genomes were determined using the pooled segment genome sequencing method combined with the Illumina sequencing platform resulting in an average coverage depth of 1,021x and 644x for the TPE Kampung Dalan K363 and TPE Sei Geringging K403 genomes, respectively. Both Indonesian TPE strains were genetically related to each other and were more distantly related to other, previously characterized TPE strains. The modular character of several genes, including TP0136 and TP0858 gene orthologs, was identified by analysis of the corresponding sequences. To systematically detect genes potentially having a modular genetic structure, we performed a whole genome analysis-of-occurrence of direct or inverted repeats of 17 or more nucleotides in length. Besides in tpr genes, a frequent presence of repeats was found in the genetic regions spanning TP0126-TP0136, TP0856-TP0858, and TP0896 genes. Conclusions/significance Comparisons of genome sequences of TPE Kampung Dalan K363 and Sei Geringging K403 with other TPE strains revealed a modular structure of several genomic loci including the TP0136, TP0856, and TP0858 genes. Diversification of TPE genomes appears to be facilitated by intra-strain genome recombination events.

Návaznosti

GA17-25455S, projekt VaV

Název: Studium genomů patogenních treponem na základě analýzy jednotlivých buněk

Investor: Grantová agentura ČR, Studium genomů patogenních treponem na základě analýzy jednotlivých buněk

GJ17-25589Y, projekt VaV

Název: Kmeny způsobující syfilis: jsou geneticky odlišné kmeny odlišné i v průběhu experimentální infekce?

Investor: Grantová agentura ČR, Genetically distinct groups of syphilis-causing strains: do they differ during experimental infection?

LM2015043, projekt VaV

Název: Česká infrastruktura pro integrativní strukturní biologii (Akronym: CIISB)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Czech Infrastructure for Integrative Structural Biology

Citovat

STROUHAL, Michal, Lenka PAŠTĚKOVÁ, Jan HAVIERNIK, Sascha KNAUF, Sylvia BRUISTEN, Gerda T. NOORDHOEK, Jan OPPELT, Darina ČEJKOVÁ a David ŠMAJS. Complete genome sequences of two strains of Treponema pallidum subsp pertenue from Indonesia: Modular structure of several treponemal genes. PLoS neglected tropical diseases. San Francisco: Public Library of Science, 2018, roč. 12, č. 10, s. 0006867-6886. ISSN 1935-2735. Dostupné z: https://dx.doi.org/10.1371/journal.pntd.0006867.

@article{1482997,
   author = {Strouhal, Michal and Paštěková, Lenka and Haviernik, Jan and Knauf, Sascha and Bruisten, Sylvia and Noordhoek, Gerda T. and Oppelt, Jan and Čejková, Darina and Šmajs, David},
   article_location = {San Francisco},
   article_number = {10},
   doi = {http://dx.doi.org/10.1371/journal.pntd.0006867},
   keywords = {Treponema pallidum subsp. pertenue},
   language = {eng},
   issn = {1935-2735},
   journal = {PLoS neglected tropical diseases},
   title = {Complete genome sequences of two strains of Treponema pallidum subsp pertenue from Indonesia: Modular structure of several treponemal genes},
   url = {https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0006867},
   volume = {12},
   year = {2018}
}

TY  - JOUR
ID  - 1482997
AU  - Strouhal, Michal - Paštěková, Lenka - Haviernik, Jan - Knauf, Sascha - Bruisten, Sylvia - Noordhoek, Gerda T. - Oppelt, Jan - Čejková, Darina - Šmajs, David
PY  - 2018
TI  - Complete genome sequences of two strains of Treponema pallidum subsp pertenue from Indonesia: Modular structure of several treponemal genes
JF  - PLoS neglected tropical diseases
VL  - 12
IS  - 10
SP  - 0006867
EP  - 0006867
PB  - Public Library of Science
SN  - 19352735
KW  - Treponema pallidum subsp. pertenue
UR  - https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0006867
N2  - Background Treponema pallidum subsp. pertenue (TPE) is the causative agent of yaws, a multistage disease endemic in tropical regions in Africa, Asia, Oceania, and South America. To date, seven TPE strains have been completely sequenced and analyzed including five TPE strains of human origin (CDC-2, CDC 2575, Gauthier, Ghana-051, and Samoa D) and two TPE strains isolated from the baboons (Fribourg-Blanc and LMNP-1). This study revealed the complete genome sequences of two TPE strains, Kampung Dalan K363 and Sei Geringging K403, isolated in 1990 from villages in the Pariaman region of Sumatra, Indonesia and compared these genome sequences with other known TPE genomes. Methodology/principal findings The genomes were determined using the pooled segment genome sequencing method combined with the Illumina sequencing platform resulting in an average coverage depth of 1,021x and 644x for the TPE Kampung Dalan K363 and TPE Sei Geringging K403 genomes, respectively. Both Indonesian TPE strains were genetically related to each other and were more distantly related to other, previously characterized TPE strains. The modular character of several genes, including TP0136 and TP0858 gene orthologs, was identified by analysis of the corresponding sequences. To systematically detect genes potentially having a modular genetic structure, we performed a whole genome analysis-of-occurrence of direct or inverted repeats of 17 or more nucleotides in length. Besides in tpr genes, a frequent presence of repeats was found in the genetic regions spanning TP0126-TP0136, TP0856-TP0858, and TP0896 genes. Conclusions/significance Comparisons of genome sequences of TPE Kampung Dalan K363 and Sei Geringging K403 with other TPE strains revealed a modular structure of several genomic loci including the TP0136, TP0856, and TP0858 genes. Diversification of TPE genomes appears to be facilitated by intra-strain genome recombination events.
ER  -

STROUHAL, Michal, Lenka PAŠTĚKOVÁ, Jan HAVIERNIK, Sascha KNAUF, Sylvia BRUISTEN, Gerda T. NOORDHOEK, Jan OPPELT, Darina ČEJKOVÁ a David ŠMAJS. Complete genome sequences of two strains of Treponema pallidum subsp pertenue from Indonesia: Modular structure of several treponemal genes. \textit{PLoS neglected tropical diseases}. San Francisco: Public Library of Science, 2018, roč.~12, č.~10, s.~0006867-6886. ISSN~1935-2735. Dostupné z: https://dx.doi.org/10.1371/journal.pntd.0006867.

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