BMX: a tool for computing bacterial phyletic composition from orthologous maps

Differences in genetic flux in invasive Streptococcus pneumoniae associated with bacteraemia and meningitis

Background

Genetic flux, a crucial process of pneumococcal evolution, is an essential aspect of bacterial physiology during human pathogenesis. However, the role of these genetic changes and the selective forces that drive them is not fully understood. Elucidating the underlying selective forces that determine the magnitude and direction (gene gain or loss) of gene transfer is important for better understanding the pathogenesis process, and may also highlight potential therapeutic and diagnostic targets.

Methods

Here, we leveraged data from high throughput genome sequencing and robust probabilistic models to discover the magnitude and likely direction of genetic flux events, but not the source, in 209 multi-lineage invasive pneumococcal genomes generated from blood (n = 147) and CSF (n = 62) isolates, associated with bacteremia and meningitis respectively. The Gain and Loss Mapping Engine (GLOOME) was used to infer gene gain and loss more accurately by taking into account differences in rates of gene gain and loss among gene families, as well as independent evolution within and across lineages.

Results

Our results show the likely extent and direction of gene fluctuations at different niche, during pneumococcal pathogenesis, highlighting that evolutionary dynamics are important for tissue-specific host invasion and survival.

Conclusion

These findings improve insights on evolutionary dynamics during invasive pneumococcal disease, and highlight potential diagnostic and therapeutic targets.

Detecting bracoviral orthologs distribution in five tsetse fly species and the housefly genomes

Objective

Mutualism between endogenous viruses and eukaryotes is still poorly understood. Several endogenous double-stranded polydnaviruses, bracoviruses, homologous to those present in parasitic braconid wasp genomes were detected in the tsetse fly (Glossina morsitans morsitans). This is peculiar since tsetse flies do not share a reproductive lifestyle similar to wasps, but deliver fully developed larvae that pupate within minutes of exiting their mothers. The objective of this study is to investigate genomic distribution of bracoviral sequences in five tsetse fly species and the housefly, and examine its value as a potential vector control strategy target point. We use comparative genomics to determine the presence, distribution across Glossina species genomes, and evolutionary relationships of bracoviruses of five tsetse fly species and the housefly.

Results

We report on homologous bracoviruses in multiple Dipteran genomes. Phylogenetic reconstruction using within-species concatenated bracoviral orthologs shows great congruence with previously reconstructed insect species phylogenies. Our findings suggest that bracoviruses present in Diptera originate from a single integration event of the viral genome that occurred in an ancestor insect before the evolutionary radiation of different insect orders.

Comparative genomics identifies male accessory gland proteins in five Glossina species

Accessory gland proteins (ACPs) are important reproductive proteins produced by the male accessory glands (MAGs) of most insect species. These proteins are essential for male insect fertility, and are transferred alongside semen to females during copulation. ACPs are poorly characterized in Glossina species (tsetse fly), the principal vector of the parasite that causes life-threatening Human African Trypanosomiasis and Animal trypanosomiasis in endemic regions in Africa. The tsetse fly has a peculiar reproductive cycle because of the absence of oviposition. Females mate once and store sperm in a spermathecal, and produce a single fully developed larva at a time that pupates within minutes of exiting their uterus. This slow reproductive cycle, compared to other insects, significantly restricts reproduction to only 3 to 6 larvae per female lifespan. This unique reproductive cycle is an attractive vector control strategy entry point. We exploit comparative genomics approaches to explore the diversity of ACPs in the recently available whole genome sequence data from five tsetse fly species ( Glossina morsitans, G. austeni, G. brevipalpis, G. pallidipes and G. fuscipes). We used previously described ACPs in Drosophila melanogaster and Anopheles gambiae as reference sequences. We identified 36, 27, 31, 29 and 33 diverse ACP orthologous genes in G. austeni, G. brevipalpis, G. fuscipes, G. pallidipes and G. morsitans genomes respectively, which we classified into 21 functional classes. Our findings provide genetic evidence of MAG proteins in five recently sequenced Glossina genomes. It highlights new avenues for molecular studies that evaluate potential field control strategies of these important vectors of human and animal disease.

Comparative genomics identifies male accessory gland proteins in five Glossina species

Accessory gland proteins (ACPs) are important reproductive proteins produced by the male accessory glands (MAGs) of most insect species. These proteins are essential for male insect fertility, and are transferred alongside semen to females during copulation. ACPs are poorly characterized in Glossina species (tsetse fly), the principal vector of the parasite that causes life-threatening Human African Trypanosomiasis and Animal trypanosomiasis in endemic regions in Africa. The tsetse fly has a peculiar reproductive cycle because of the absence of oviposition. Females mate once and store sperm in a spermathecal, and produce a single fully developed larva at a time that pupates within minutes of exiting their uterus. This slow reproductive cycle, compared to other insects, significantly restricts reproduction to only 3 to 6 larvae per female lifespan. This unique reproductive cycle is an attractive vector control strategy entry point. We exploit comparative genomics approaches to explore the diversity of ACPs in the recently available whole genome sequence data from five tsetse fly species (Glossina morsitans, G. austeni, G. brevipalpis, G. pallidipes and G. fuscipes). We used previously described ACPs in Drosophila melanogaster and Anopheles gambiae as reference sequences. We identified 36, 27, 31, 29 and 33 diverse ACP orthologous genes in G. austeni, G. brevipalpis, G. fuscipes, G. pallidipes and G. morsitans genomes respectively, which we classified into 21 functional classes. Our findings provide genetic evidence of MAG proteins in five recently sequenced Glossina genomes. It provides new avenues for molecular studies that evaluate potential field control strategies of these important vectors of human and animal disease.