Ribosomal depletion in B. malayi

Here, we compared ribosomal depletion methods in Brugia malayi (B. malayi) containing the symbiotic endosymbiont Wolbachia. We sequenced total RNA, Terminator exonuclease treated RNA, ribosomal depletion with the NEBNext Human/Mouse/Rat/ Bacterial ribosomal depletion kits and with a custom depletion probe set designed specifically against the B. malayi and Wolbachia rRNA genes. The total RNA libraries had over 80% of reads mapping to ribosomal genes. The Terminator and NEBNext depletion libraries each had around 30% ribosomal reads. We found the most efficient depletion with the custom probe set, with only 0.23% of rRNA reads remaining. Additionally, the custom depletion set resulted in a 300-fold increase in Wolbachia mRNA reads compared to the total RNA-seq library. We also sequenced total and custom depletion libraries in C. elegans and D. immitis nematodes. The B. malayi probes resulted in parital depletion from C. elegans but almost complete removal of rRNA reads from the D. immits sample, with only 0.3% of reads mapping to ribosomal genes. The B. malayi custom probes work as a pan-filarial ribosomal depletion method.