Screening Host Genomic Data for Wolbachia Infections.

Autor:	Valerio F; Insect Symbiosis Ecology and Evolution, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.; Research Centre for Ecological Changes, University of Helsinki, Helsinki, Finland., Twort VG; The Finnish Museum of Natural History, Luomus, University of Helsinki, Helsinki, Finland., Duplouy A; Insect Symbiosis Ecology and Evolution, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland. anne.duplouy@helsinki.fi.; Research Centre for Ecological Changes, University of Helsinki, Helsinki, Finland. anne.duplouy@helsinki.fi.
Jazyk:	angličtina
Zdroj:	Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2024; Vol. 2739, pp. 251-274.
DOI:	10.1007/978-1-0716-3553-7_16
Abstrakt:	Less than a decade ago, the production of Wolbachia genomic assemblies was tedious, time-consuming, and expensive. The production of Wolbachia genomic DNA free of contamination from host DNA, as required for Wolbachia-targeted sequencing, was then only possible after the amplification and extraction of a large amount of clonal Wolbachia DNA. However, as an endosymbiotic bacterium, Wolbachia does not grow outside the host cell environment, and large-scale recovery of the bacteria required mass rearing of their host, preferably clones of a single individual to avoid strain genetic diversity, or amplification of cell cultures infected with a single Wolbachia strain. Bacterial DNA could be separated from host DNA based on genomic size. Nowadays, the production of full Wolbachia genomes does not require the physical isolation of the bacterial strains from their respective hosts, and the bacterium is often sequenced as a by-catch of host genomic projects. Here, we provide a step-by-step protocol to (1) identify whether host genome projects contain reads from associated Wolbachia and (2) isolate/retrieve the Wolbachia reads from the rest of the sequenced material. We hope this simple protocol will support many projects aiming at studying diverse Wolbachia genome assemblies. (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
Databáze:	MEDLINE
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