Dynamic but Constrained: Repeated Acquisitions of Nutritional Symbionts in Cimicidae from a Narrow Taxonomic Pool
Description
The project analyzes phylogeny of symbiotic bacteria associated with Cimicidae, reconstruct cospeciation histories and metabolic dependences.
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Steps to reproduce
Based on results of amplicons 14 Cimicidae species were chosen for metagenomic sequencing. The shotgun genomic libraries were prepared from enriched gDNAs, multiplexed and sequenced on SP lanes of NovaSeg 6000 from both ends. Metagenomic raw reads were quality trimmed using Trimmomatic (Bolger, Lohse and Usadel 2014) with -phred33 option and assembled with SPades. From each successful assembly, a BLAST database was created and screened for contigs corresponding to symbionts indicated by the amplicon data: Wolbachia, Symbiopectobacterium, Sodalis, Serratia, and Tisiphia. To obtain representative queries, we downloaded genomes from NCBI that covered the diversity of each of these four bacterial taxa.
Institutions
- Jihoceska Univerzita v Ceskych Budejovicich Prirodovedecka Fakulta
- Ceska Zemedelska Univerzita v Praze