New paper on the value of honey bee short read data in symbiont research

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/ 

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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.

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