Our work on Spiroplasma evolution in Drosophila is now available as a preprint here. This is the first publication from my postdoctoral work with Greg Hurst at the University of Liverpool. It was also a very nice collaboration with great people from Liverpool, Texas A&M and EPFL. The work was funded by the European Union’s Horizon 2020 Research and Innovation Program under Marie Sklodowska-Curie grant agreement 703379.
Spiroplasma is a very interesting symbiont with lots of peculiar features (I'd recommend these reviews about its biology). After some mostly anecdotal evidence that Spiroplasma symbionts evolve quickly, we here have determined Spiroplasma mutational rates systematically. We find that indeed, Spiroplasma can be considered a hypermutator, especially when compared with Wolbachia (the only other natural inherited symbiont of Drosophila). There are some interesting implications for Spiroplasma evolutionary ecology that arise from this which we discuss in the manuscript. We also show and discuss lots of comparative genomics data.
If you want to learn more, please have a look at the video below which is a recording of my presentation about this work from the Symbiosis Seminar Series organised by Nicole Gerardo and Greg Hurst.
This post is a ‘behind the paper’ story of our publication ‘Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity’ which was just published in PeerJ. I will explain the motivation behind the study and also show some new data generated with our approach.
UPDATE (July 24, 2017): Our paper was covered in the "The Molecular Ecologist" blog: http://www.molecularecologist.com/2017/07/genomes-are-coming-sequence-libraries-from-the-honey-bee-reflect-associated-microbial-diversity/
Part one: background & motivation
I work as a postdoc in Greg Hurst’s group, who has projects on many different bacterial symbionts (https://sites.google.com/site/hurstlab/home). The project of his PhD student Georgia Drew aims to identify the potential impacts of Arsenophonus on honey bee health (https://eegid.wordpress.com/phd-students/georgia-drew/). This bacterium is an inherited symbiont of arthropods, and has been found in honey bees and other bees occasionally (Aizenberg-Gershtein et al. 2013; Gerth et al. 2015; Yañez et al. 2016; McFrederick et al. 2017). Its exact role in honey bees is unclear, and this is what Georgia studies.
I became involved when Greg suggested to extract genomic data of the honey bee associated Arsenophonus from Apis Illumina data stored public databases. In many cases, symbionts are sequenced inadvertently alongside with their hosts, and a number of symbiont genomes have been extracted from sequencing data of their hosts before (e.g., Salzberg et al. 2005; Siozios et al. 2013). There’s plenty of honey bee sequencing data around, so it was definitely worth checking if we could get an Arsenophonus genome ‘for free’, without actually sequencing it ourselves.
New paper on Wolbachia genomics
Our new paper "Comparative genomics provides a timeframe for Wolbachia evolution and exposes a recent biotin synthesis operon transfer" was published today!
Check out the paper here: www.nature.com/articles/nmicrobiol2016241 – please email me for a pdf of this article!
I also wrote a short "Behind the paper" blogpost for the Nature Microbiology Community website.
Read it here:
EDIT (July 12, 2017): You can access the paper for free under http://rdcu.be/t8tX
Novel, 'exotic' Wolbachia genomes
This post deals with a recent paper about Wolbachia in plant parasitic nematodes, and with Wolbachia phylogeny in general.
Almost 30 genomes of the bacterial endosymbiont Wolbachia have been sequenced so far, and this trend is likely to continue. Wolbachia are found in a large proportion of arthropods (insects, arachnids, and allies) and in filarial nematodes. Very generally speaking, Wolbachia in arthropods are opportunistic, with varied fitness effects for their hosts, and may switch hosts horizontally. In contrast, Wolbachia in filarials are highly specialized and absolutely required for their hosts (the mechanisms underlying this co-dependence are not 100% clear yet).
The differences in lifestyle of Wolbachia from arthropods and filarials is also reflected in their genomic architecture. For example, arthropod Wolbachia typically harbour many mobile genetic elements (e.g, insertion sequences, prophages & other phage-derived elements) that are almost always missing in the very streamlined and reduced filarial Wolbachia genomes.
Now, for the first time, there is genomic data from more 'exotic' Wolbachia strains: Brown et al. have sequenced the genome of Wolbachia from a plant-parasitic nematode (wPpe from Pratylenchus penetrans), and, in a recent publication (Brown et al. 2016) compare it to the rest of the genomes of Wolbachia from arthropods and filarial nematodes. They also include in their analysis a strain from the banana aphid (wPni from Pentalonia nigronervosa) and a springtail (wFol from Folsomia candida). These strains were sequenced previously (De Clerck et al. 2015 & Gerth et al. 2014, respectively), but never investigated in a comparative framework before. All three strains are genetically very divergent from typical arthropod and filarial Wolbachia, so it was really cool to see this analysis published.
Here, I want to briefly summarize the main findings of Brown et al.' s study and comment on what phylogenomic datasets and gene repertoires can tell us about evolutionary relationships within Wolbachia.
This is the website of Michael Gerth. I am a biologist with an interest in insects and the microbes within them. Click here to learn more.