Authors
A Bacigalupo2; P Schwabl2; D C Hernández4; K Brunker2; J D Ramírez4; L E Hernandez-Castro3; B Cheaib2; A G Villacís5; M J Grijalva1; K R Elmer2; M S Llewellyn2; 1 Ohio University, United States; 2 Institute of Biodiversity, Animal Health and comparative Medicine, University of Glasgow, UK; 3 The Roslin Institute, University of Edinburgh, UK; 4 Facultad de Ciencias Naturales, Universidad del Rosario, Colombia; 5 Centro de Investigación para la Salud en América Latina, Pontificia Universidad Católica del Ecuador, Ecuador Discussion
Chagas disease or American trypanosomiasis is a chronic illness caused by the protozoan Trypanosoma cruzi. It is transmitted to mammals by hematophagous insect vectors of the Subfamily Triatominae (Hemiptera: Reduviidae), comprising more than 150 species. Remarkably, only three genomes of triatomine species are available. More genomes will enable the study of the biology, ecology and evolution of individual species, and the Subfamily in general. The goal of this study is to provide new genomic information about Rhodnius ecuadoriensis, the main vector of Chagas disease in Ecuador and Northern Peru. This species maintains domestic, peridomestic and sylvatic populations, presenting high T. cruzi infection rates.
DNA from one R. ecuadoriensis was extracted using a commercial kit and it was sequenced using two approaches: Oxford Nanopore in a MinION flowcell to obtain long reads, and Illumina HiSeq for short reads. The hybrid assembler MaSuRCA 3.3.9 was used to incorporate both read types in the assembly; a second assembly was produced by MaSuRCA, with the same short reads, but including filtered Nanopore reads by read length. The draft genomes were evaluated by an intrinsic quality assessment, describing the proportion of the genome included in the assembly. The selected genome assembly was improved using SSPACE Standard 3.0 for extending contigs and scaffolding. Later, the completeness of the resulting draft assembly was quantified by the accurate presence of single-copy orthologous from Insecta (insecta_odb10) and Hemiptera (hemiptera_odb10) lineage databases using benchmarking universal single-copy ortholog genes BUSCO 4.0.6 and compared to those of available triatomine genomes.
A total of 47.1 million Illumina paired reads of 150 bp each and 1,506,368 Oxford Nanopore reads were obtained from the same R. ecuadoriensis individual, and their GC content was ~34%. The unfiltered draft assembly of R. ecuadoriensis produced a higher quality assembly than the one with filtered long reads, taking into account total number of scaffolds, average scaffold size, N50 and E-size. The use of SSPACE improved genome contiguity of the unfiltered draft genome. When comparing BUSCOs using the Insecta database, this draft R. ecuadoriensis genome had the highest completeness (96.4%), compared with 95.7% from Triatoma rubrofasciata, 95.5% from R. prolixus, and 90.4% from T. infestans. Using the Hemiptera database, it was second with 97% completeness, behind R. prolixus (98.2%); T. rubrofasciata (95.7%) and T. infestans (91.6%) followed.
Genomics of vectors can provide clues on targets to prevent and control vectorial diseases. Using a short and long read combined approach, we have produced a draft assembly of R. ecuadoriensis that shows comparable quality in terms of completeness to previously published triatomine genomes. Transcriptomics and genome annotation are now underway. Funding: ANID/Programa Becas/Doctorado Becas Chile 2019 72200391. 
