Hybrid short- and long-read assembly of an experimentally evolved Sodalis glossinidius strain SgGmmC1*

Abstract

Bacterial symbionts of insects undergo dramatic genome reduction during their evolutionary transition from free-living to host-dependent lifestyles, but the dynamics of this process remain poorly understood due to the difficulty of observing these processes in real-time. Sodalis glossinidius, a facultative 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%), 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 after ten years of serial passaging in laboratory culture (SgGmmC1*) to a counterpart isolated at the same time (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 similar. Comparative analysis revealed a significant deletion (17,209 bp) containing 31 genes, including (involved in thiamine biosynthesis) and genes encoding sulfur transporters. Additionally, we identified multiple small-scale mutations (8 deletions, 39 insertions, 10 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 paratransgenic approaches using S. glossinidius for trypanosome control. DATA SUMMARYRaw Nanopore and MiSeq reads are available in the European Nucleotide Archive under Project PRJEB32321 (Read accessions: ERX3321202 and ERX3321201 respectively). A full GBK formatted annotation of SgGmmC1* has been deposited in Figshare at https://doi.org/10.17866/rd.salford.8052437.v1. IMPACT STATEMENTIn this study we provide new insights into the ongoing genome degradation of Sodalis glossinidius, a facultative endosymbiont of tsetse flies implicated in their ability to transmit trypanosomiasis, during prolonged laboratory culture. Through high-quality comparative genomics we reveal significant gene loss and mutational changes, including disruption of pathways involved in nutrient biosynthesis. These findings enhance our understanding of symbiont genome evolution and inform the development of S. glossinidius as a potential tool for paratransgenic strategies in controlling trypanosome transmission.