Laboratory evolution drives continued genome degradation in the facultative tsetse symbiont Sodalis glossinidius
- 1Faculty of Health, Community and Life Sciences, University of Salford, Salford, United Kingdom
- 2Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- 3Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
Abstract
Bacterial symbionts of insects undergo dramatic genome reduction during their evolutionary transition from free-living to host-dependent lifestyles, but the dynamics of genome degradation remain poorly understood due to the difficulty of observing these processes in real-time. Sodalis glossinidius, a facultative bacterial endosymbiont of tsetse flies, provides an exceptional opportunity to study this transition experimentally: Unlike highly specialised obligate symbionts, S. glossinidius can be cultured in vitro and retains a large genome (4 Mbp) with extensive pseudogene content (49%, vs. ~ 1% in free-living bacteria), suggesting a recent evolutionary transition. Here, we present a comparative genomic analysis of S. glossinidius strains isolated from laboratory colony-derived Glossina morsitans morsitans, comparing one strain after ten years of serial passaging in laboratory culture (SgGmmC1*) to a counterpart isolated at the same time from the same colony (SgGmmB4). Hybrid genome assembly using Oxford Nanopore and Illumina technologies produced a high-quality 4.29 Mbp genome comprising one circular chromosome and four plasmids. Comparative analysis revealed a significant deletion (16,493 bp) containing 31 genes, including thiM (involved in thiamine biosynthesis) and genes encoding sulfur transporters. Additionally, we identified multiple small-scale chromosomal mutations (8 deletions, 39 insertions, 11 SNPs) resulting in frameshifts in genes including a hemolysin precursor (shlA). Our findings demonstrate that, under stable laboratory conditions without the selective pressures of the host environment, S. glossinidius continues to undergo genome degradation. The loss of thiM supports previous hypotheses of complementary metabolic pathways between S. glossinidius and the primary symbiont Wigglesworthia glossinidia for thiamine biosynthesis. This study provides insights into the evolutionary trajectory of facultative symbionts and has implications for studying the patterns of genome evolution in bacterial symbionts adapting to novel ecological niches, as well as paratransgenic approaches using S. glossinidius for trypanosome control. Author summary: Bacteria that live inside insects often start out as free-living organisms but, over millions of years, become permanently dependent on their host. As this happens, their genomes reduce in size: genes that are no longer needed are first disrupted (pseudogenised) and then lost entirely (deleted). Although we can see the end results of this process by comparing the genomes of different symbiotic bacteria, directly observing it as it happens is extremely difficult because it normally unfolds over vast timescales. In this study, we took advantage of a rare opportunity to observe patterns of genome reduction. Sodalis glossinidius is a bacterium that lives inside tsetse flies, the insect responsible for transmitting sleeping sickness in sub-Saharan Africa. Unlike most insect symbionts, it can be grown in the laboratory. We compared the genome of a strain that had been grown in laboratory culture for ten years against a closely related strain kept in frozen storage, and found that the cultured strain had lost a substantial stretch of DNA containing 31 genes, alongside several smaller mutations that disrupted additional genes. These findings deepen our understanding of how symbiotic bacteria evolve and have practical implications for efforts to use S. glossinidius as a tool for controlling the spread of Sleeping Sickness and animal trypanosomiasis.
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BibTeX
@article{pescod2026laboratory,
title = {{Laboratory evolution drives continued genome degradation in the facultative tsetse symbiont Sodalis glossinidius}},
author = {Poppy Pescod and Lee R. Haines and Alistair C. Darby and Ian Goodhead},
journal = {PLOS Neglected Tropical Diseases},
year = {2026},
month = sep,
doi = {10.1371/journal.pntd.0014725},
url = {https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014725},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Laboratory evolution drives continued genome degradation in the facultative tsetse symbiont Sodalis glossinidius
AU - Poppy Pescod
AU - Lee R. Haines
AU - Alistair C. Darby
AU - Ian Goodhead
PY - 2026
DA - 2026/09/15
JO - PLOS Neglected Tropical Diseases
DO - 10.1371/journal.pntd.0014725
UR - https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014725
AB - Bacterial symbionts of insects undergo dramatic genome reduction during their evolutionary transition from free-living to host-dependent lifestyles, but the dynamics of genome degradation remain poorly understood due to the difficulty of observing these processes in real-time. Sodalis glossinidius, a facultative bacterial endosymbiont of tsetse flies, provides an exceptional opportunity to study this transition experimentally: Unlike highly specialised obligate symbionts, S. glossinidius can be cultured in vitro and retains a large genome (4 Mbp) with extensive pseudogene content (49%, vs. ~ 1% in free-living bacteria), suggesting a recent evolutionary transition. Here, we present a comparative genomic analysis of S. glossinidius strains isolated from laboratory colony-derived Glossina morsitans morsitans, comparing one strain after ten years of serial passaging in laboratory culture (SgGmmC1*) to a counterpart isolated at the same time from the same colony (SgGmmB4). Hybrid genome assembly using Oxford Nanopore and Illumina technologies produced a high-quality 4.29 Mbp genome comprising one circular chromosome and four plasmids. Comparative analysis revealed a significant deletion (16,493 bp) containing 31 genes, including thiM (involved in thiamine biosynthesis) and genes encoding sulfur transporters. Additionally, we identified multiple small-scale chromosomal mutations (8 deletions, 39 insertions, 11 SNPs) resulting in frameshifts in genes including a hemolysin precursor (shlA). Our findings demonstrate that, under stable laboratory conditions without the selective pressures of the host environment, S. glossinidius continues to undergo genome degradation. The loss of thiM supports previous hypotheses of complementary metabolic pathways between S. glossinidius and the primary symbiont Wigglesworthia glossinidia for thiamine biosynthesis. This study provides insights into the evolutionary trajectory of facultative symbionts and has implications for studying the patterns of genome evolution in bacterial symbionts adapting to novel ecological niches, as well as paratransgenic approaches using S. glossinidius for trypanosome control. Author summary: Bacteria that live inside insects often start out as free-living organisms but, over millions of years, become permanently dependent on their host. As this happens, their genomes reduce in size: genes that are no longer needed are first disrupted (pseudogenised) and then lost entirely (deleted). Although we can see the end results of this process by comparing the genomes of different symbiotic bacteria, directly observing it as it happens is extremely difficult because it normally unfolds over vast timescales. In this study, we took advantage of a rare opportunity to observe patterns of genome reduction. Sodalis glossinidius is a bacterium that lives inside tsetse flies, the insect responsible for transmitting sleeping sickness in sub-Saharan Africa. Unlike most insect symbionts, it can be grown in the laboratory. We compared the genome of a strain that had been grown in laboratory culture for ten years against a closely related strain kept in frozen storage, and found that the cultured strain had lost a substantial stretch of DNA containing 31 genes, alongside several smaller mutations that disrupted additional genes. These findings deepen our understanding of how symbiotic bacteria evolve and have practical implications for efforts to use S. glossinidius as a tool for controlling the spread of Sleeping Sickness and animal trypanosomiasis.
SN - 1935-2735
ER -