The power of whole-genome sequencing for epidemiology remains throttled by parasite sample quality and quantity.
Parasite cells are inherently tethered to vector/host tissue, typically swamped by orders of magnitude in contaminating material that challenges direct extraction and cedes too little sample to sequence. Follow-up cell culture often proves ineffective, many costly ex vivo systems raising more bias and frustration then parasite.
To bypass this laboratory bottleneck in the landscape genomics of Chagas disease, we are developing a magnetic-capture-hybridization protocol to recover genome-wide information on Trypanosoma cruzi directly from its arthropod vector. We target an idiosyncrasy of trypanosomatid gene expression, the 39-nucleotide “spliced leader” sequence that primes each RNA message for translation, to bait the transcriptome all at once for RNAseq without prior parasite extraction or culture.
Employing a variety of sample types, we examine our method’s performance (sensitivity, reproducibility, bias, etc.) and its ultimate reach…
RAD-like reduced representation for landscape genomics – or more?
