Abstract
Orientia tsutsugamushi, formerly Rickettsia tsutsugamushi, is an obligate intracellular pathogen that causes scrub typhus, an underdiagnosed acute febrile disease with high morbidity. Scrub typhus is transmitted by the larval stage (chigger) of Leptotrombidium mites and is irregularly distributed across endemic regions of Asia, Australia and islands of the western Pacific Ocean. Previous work to understand population genetics in O. tsutsugamushi has been based on sub-genomic sampling methods and whole-genome characterization of two genomes. In this study, we compared 40 genomes from geographically dispersed areas and confirmed patterns of extensive homologous recombination likely driven by transposons, conjugative elements and repetitive sequences. High rates of lateral gene transfer (LGT) among O. tsutsugamushi genomes appear to have effectively eliminated a detectable clonal frame, but not our ability to infer evolutionary relationships and phylogeographical clustering. Pan-genomic comparisons using 31 082 high-quality bacterial genomes from 253 species suggests that genomic duplication in O. tsutsugamushi is almost unparalleled. Unlike other highly recombinant species where the uptake of exogenous DNA largely drives genomic diversity, the pan-genome of O. tsutsugamushi is driven by duplication and divergence. Extensive gene innovation by duplication is most commonly attributed to plants and animals and, in contrast with LGT, is thought to be only a minor evolutionary mechanism for bacteria. The near unprecedented evolutionary characteristics of O. tsutsugamushi, coupled with extensive intra-specific LGT, expand our present understanding of rapid bacterial evolutionary adaptive mechanisms.
| Original language | English (US) |
|---|---|
| Journal | Microbial genomics |
| Volume | 4 |
| Issue number | 9 |
| DOIs | |
| State | Published - Sep 1 2018 |
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Keywords
- adaptive evolution
- gene divergence
- genome adaptation
- lateral gene transfer
- pan-genome
- scrub typhus
ASJC Scopus subject areas
- Medicine(all)
Cite this
Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity. / Fleshman, Amy; Mullins, Kristin; Sahl, Jason; Hepp, Crystal; Nieto, Nathan C; Wiggins, Kristin; Hornstra, Heidie; Kelly, Daryl; Chan, Teik Chye; Phetsouvanh, Rattanaphone; Dittrich, Sabine; Panyanivong, Phonepasith; Paris, Daniel; Newton, Paul; Richards, Allen; Pearson, Talima R.
In: Microbial genomics, Vol. 4, No. 9, 01.09.2018.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity
AU - Fleshman, Amy
AU - Mullins, Kristin
AU - Sahl, Jason
AU - Hepp, Crystal
AU - Nieto, Nathan C
AU - Wiggins, Kristin
AU - Hornstra, Heidie
AU - Kelly, Daryl
AU - Chan, Teik Chye
AU - Phetsouvanh, Rattanaphone
AU - Dittrich, Sabine
AU - Panyanivong, Phonepasith
AU - Paris, Daniel
AU - Newton, Paul
AU - Richards, Allen
AU - Pearson, Talima R
PY - 2018/9/1
Y1 - 2018/9/1
N2 - Orientia tsutsugamushi, formerly Rickettsia tsutsugamushi, is an obligate intracellular pathogen that causes scrub typhus, an underdiagnosed acute febrile disease with high morbidity. Scrub typhus is transmitted by the larval stage (chigger) of Leptotrombidium mites and is irregularly distributed across endemic regions of Asia, Australia and islands of the western Pacific Ocean. Previous work to understand population genetics in O. tsutsugamushi has been based on sub-genomic sampling methods and whole-genome characterization of two genomes. In this study, we compared 40 genomes from geographically dispersed areas and confirmed patterns of extensive homologous recombination likely driven by transposons, conjugative elements and repetitive sequences. High rates of lateral gene transfer (LGT) among O. tsutsugamushi genomes appear to have effectively eliminated a detectable clonal frame, but not our ability to infer evolutionary relationships and phylogeographical clustering. Pan-genomic comparisons using 31 082 high-quality bacterial genomes from 253 species suggests that genomic duplication in O. tsutsugamushi is almost unparalleled. Unlike other highly recombinant species where the uptake of exogenous DNA largely drives genomic diversity, the pan-genome of O. tsutsugamushi is driven by duplication and divergence. Extensive gene innovation by duplication is most commonly attributed to plants and animals and, in contrast with LGT, is thought to be only a minor evolutionary mechanism for bacteria. The near unprecedented evolutionary characteristics of O. tsutsugamushi, coupled with extensive intra-specific LGT, expand our present understanding of rapid bacterial evolutionary adaptive mechanisms.
AB - Orientia tsutsugamushi, formerly Rickettsia tsutsugamushi, is an obligate intracellular pathogen that causes scrub typhus, an underdiagnosed acute febrile disease with high morbidity. Scrub typhus is transmitted by the larval stage (chigger) of Leptotrombidium mites and is irregularly distributed across endemic regions of Asia, Australia and islands of the western Pacific Ocean. Previous work to understand population genetics in O. tsutsugamushi has been based on sub-genomic sampling methods and whole-genome characterization of two genomes. In this study, we compared 40 genomes from geographically dispersed areas and confirmed patterns of extensive homologous recombination likely driven by transposons, conjugative elements and repetitive sequences. High rates of lateral gene transfer (LGT) among O. tsutsugamushi genomes appear to have effectively eliminated a detectable clonal frame, but not our ability to infer evolutionary relationships and phylogeographical clustering. Pan-genomic comparisons using 31 082 high-quality bacterial genomes from 253 species suggests that genomic duplication in O. tsutsugamushi is almost unparalleled. Unlike other highly recombinant species where the uptake of exogenous DNA largely drives genomic diversity, the pan-genome of O. tsutsugamushi is driven by duplication and divergence. Extensive gene innovation by duplication is most commonly attributed to plants and animals and, in contrast with LGT, is thought to be only a minor evolutionary mechanism for bacteria. The near unprecedented evolutionary characteristics of O. tsutsugamushi, coupled with extensive intra-specific LGT, expand our present understanding of rapid bacterial evolutionary adaptive mechanisms.
KW - adaptive evolution
KW - gene divergence
KW - genome adaptation
KW - lateral gene transfer
KW - pan-genome
KW - scrub typhus
UR - http://www.scopus.com/inward/record.url?scp=85055776989&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85055776989&partnerID=8YFLogxK
U2 - 10.1099/mgen.0.000199
DO - 10.1099/mgen.0.000199
M3 - Article
C2 - 30035711
AN - SCOPUS:85055776989
VL - 4
JO - Microbial genomics
JF - Microbial genomics
SN - 2057-5858
IS - 9
ER -