A bioinformatics approach to identifyingWolbachiainfections in arthropods

Abstract

Wolbachia is the most widespread endosymbiont, infecting >20% of arthropod species, and capable of drastically manipulating the host’s reproductive mechanisms. Conventionally, diagnosis has relied on PCR amplification; however, PCR is not always a reliable diagnostic technique due to primer specificity, strain diversity, degree of infection and/or tissue sampled. Here, we look for evidence of Wolbachia infection across a wide array of arthropod species using a bioinformatic approach to detect the Wolbachia genes ftsZ, wsp, and the groE operon in next-generation sequencing samples available through the NCBI Sequence Read Archive. For samples showing signs of infection, we attempted to assemble entire Wolbachia genomes, and in order to better understand the relationships between hosts and symbionts, phylogenies were constructed using the assembled gene sequences. Out of the 34 species with positively identified infections, eight species of arthropod had not previously been recorded to harbor Wolbachia infection. All putative infections cluster with known representative strains belonging to supergroup A or B, which are known to only infect arthropods. This study presents an efficient bioinformatic approach for post-sequencing diagnosis and analysis of Wolbachia infection in arthropods.

Is Anopheles gambiae a natural host of Wolbachia?

“…Our interpretation is in line with a recent discovery of a highly prevalent supergroup B Wolbachia strain, distinct from other supergroup B strains, in Anopheles “species A” (31). Our phylogenomic reconstructions further support this, as they place the newly assembled Wolbachia genome (33) within supergroup B, but separate from most other strains of this lineage (Fig. S1C).…”

“…Here, we examine the evidence on natural Wolbachia infections in Anopheles gambiae mosquitos and screen 1000 Anopheles genomes ( Ag1000G) project data (32) to reveal that Wolbachia reads are extremely rare in this rich and randomized dataset. We re-analyze the data from which a genome of the putative Wolbachia endosymbiont of Anopheles gambiae was assembled (33) to show that the majority of reads in the sample originate from known Wolbachia hosts different than Anopheles gambiae . Finally, we discuss the requirements to diagnose a Wolbachia infections in a species previously considered uninfected, the potential ecological interactions which could lead to the observed Wolbachia sequence prevalence patterns, and their relevance for the design of successful, integrative approaches to limit malaria spread.…”

Combined effects of elevated CO2 concentration and Wolbachia on Hylyphantes graminicola (Araneae: Linyphiidae)

“…Wolbachia infection was widely distributed in arthropods, and bioinformatics approach was essential for sequencing of Wolbachia strains which showed that most of Wolbachia belongs to subgroup A or B in most of arthropods (Pascar & Chandler, 2018). Wolbachia infection was widely distributed in arthropods, and bioinformatics approach was essential for sequencing of Wolbachia strains which showed that most of Wolbachia belongs to subgroup A or B in most of arthropods (Pascar & Chandler, 2018).…”

Complete genome assemblies for three variants of the Wolbachia endosymbiont of Drosophila melanogaster

“…(11, 12)). Successful de novo assembly 48 of complete Wolbachia genomes directly from unenriched long-read sequences also 49 demonstrates that it is unnecessary to computationally filter symbiont reads from 50 host reads based on similarity to Wolbachia reference genomes prior to assembly 51 (13,14). As the cost of long-read sequencing decreases, we argue that direct sequencing…”