AUTHOR=Kaur Taranjot , Brown Amanda M.V. 

TITLE=Discovery of a novel Wolbachia in Heterodera expands nematode host distribution

JOURNAL=Frontiers in Microbiology

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1446506

DOI=10.3389/fmicb.2024.1446506

ISSN=1664-302X

ABSTRACT=<p>Bioinformatics sequence data mining can reveal hidden microbial symbionts that might normally be filtered and removed as contaminants. Data mining can be helpful to detect <italic>Wolbachia</italic>, a widespread bacterial endosymbiont in insects and filarial nematodes whose distribution in plant-parasitic nematodes (PPNs) remains underexplored. To date, <italic>Wolbachia</italic> has only been reported a few PPNs, yet nematode-infecting <italic>Wolbachia</italic> may have been widespread in the evolutionary history of the phylum based on evidence of horizontal gene transfers, suggesting there may be undiscovered <italic>Wolbachia</italic> infections in PPNs. The goal of this study was to more broadly sample PPN <italic>Wolbachia</italic> strains in tylenchid nematodes to enable further comparative genomic analyses that may reveal <italic>Wolbachia’s</italic> role and identify targets for biocontrol. Published whole-genome shotgun assemblies and their raw sequence data from 33 <italic>Meloidogyne</italic> spp. assemblies, seven <italic>Globodera</italic> spp. assemblies, and seven <italic>Heterodera</italic> spp. assemblies were analyzed to look for <italic>Wolbachia</italic>. No <italic>Wolbachia</italic> was found in <italic>Meloidogyne</italic> spp. and <italic>Globodera</italic> spp., but among seven genome assemblies for <italic>Heterodera</italic> spp., an <italic>H. schachtii</italic> assembly from the Netherlands was found to have a large <italic>Wolbachia-</italic>like sequence that, when re-assembled from reads, formed a complete, circular genome. Detailed analyses comparing read coverage, GC content, pseudogenes, and phylogenomic patterns clearly demonstrated that the <italic>H. schachtii Wolbachia</italic> represented a novel strain (hereafter, denoted <italic>w</italic>Het). Phylogenomic tree construction with PhyloBayes showed <italic>w</italic>Het was most closely related to another PPN <italic>Wolbachia, w</italic>Tex, while 16S rRNA gene analysis showed it clustered with other <italic>Heterodera Wolbachia</italic> assembled from sequence databases. Pseudogenes in <italic>w</italic>Het suggested relatedness to the PPN clade, as did the lack of significantly enriched GO terms compared to PPN <italic>Wolbachia</italic> strains. It remains unclear whether the lack of <italic>Wolbachia</italic> in other published <italic>H. schachtii</italic> isolates represents the true absence of the endosymbiont from some hosts.</p>