Community genomics of the Chagas Disease vector, Triatoma dimidiata: uncovering genetic variation and gut microbial fauna of a deadly kissing bug

Chagas Disease is a human illness endemic to Latin America and caused by the parasite Trypanosoma cruzi. Multiple insects from the Triatominae sub-family transmit the disease, including Triatoma dimidiata, the predominant vector in Central America. We used Restriction-site Associated DNA Sequencing (RAD-Seq) to analyze the DNA from thirty-two T. dimidiata samples collected across Central America.  DNA was obtained from the lower abdomen of the insects to uncover genetic variation of the vector and the parasite, identify vertebrate blood meals, and assess the microbial diversity present in the insects’ hindgut. Raw sequence reads were mapped to the vector and the T. cruzi genome to obtain single nucleotide polymorphisms (SNPs). We identified 5631 SNPs from the vector, with significant spatial clustering at the regional scale as well as more locally among departments and villages within Guatemala. A total of 719 T. cruzi SNPS were found in the six specimens known to be infected with the parasite. Population genetic structure of the parasite resembled closely that found from the vector. BLAST searches identified human, rat and chicken as the most frequent blood meal sources. An estimate of 18 percent of reads not attributed to either the vector or parasite corresponded to bacterial fauna, while more than 50 percent were viral, predominantly Invertebrate iridescent virus type 6 (IIV-6). The use of RAD-seq allowed us to simultaneously retrieve high-resolution information at different geographical scales and across multiple taxa. This tool will enable future assessment of host-parasite genetics and detailed characterization of gut composition.