Journal Article

Nanopore adaptive sampling for targeted mitochondrial genome sequencing and bloodmeal identification in hematophagous insects

Lindsey, Laramie L., Faulk, Christopher, Larsen, Peter A., Blanco, Cristina M., Baker, Julia P., Milstein, Marissa S., Oliver, Jonathan D., Kipp, Evan J.

2023

Overview

Background Blood-feeding insects are important vectors for an array of zoonotic pathogens. While previous efforts toward generating molecular resources have largely focused on major vectors of global medical and veterinary importance, molecular data across a large number of hematophagous insect taxa remain limited. Advancements in long-read sequencing technologies and associated bioinformatic pipelines provide new opportunities for targeted sequencing of insect mitochondrial (mt) genomes. For engorged hematophagous insects, such technologies can be leveraged for both insect mitogenome genome assembly and identification of vertebrate blood-meal sources. Methods We used nanopore adaptive sampling (NAS) to sequence genomic DNA from four species of field-collected, blood-engorged mosquitoes ( Aedes and Culex spp. ) and one deer fly ( Chrysops sp.). NAS was used for bioinformatical enrichment of mtDNA reads of hematophagous insects and potential vertebrate blood-meal hosts using publically available mt genomes as references. We also performed an experimental control to compare results of traditional non-NAS nanopore sequencing to the mt genome enrichment by the NAS method. Results Complete mitogenomes were assembled and annotated for all five species sequenced with NAS: Aedes trivittatus, Aedes vexans , Culex restuans , Culex territans and the deer fly, Chrysops niger . In comparison to data generated during our non-NAS control experiment, NAS yielded a substantially higher proportion of reference-mapped mtDNA reads, greatly streamlining downstream mitogenome assembly and annotation. The NAS-assembled mitogenomes ranged in length from 15,582 to 16,045 bp, contained between 78.1% and 79.0% A + T content and shared the anticipated arrangement of 13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs. Maximum likelihood phylogenies were generated to further characterize each insect species. Additionally, vertebrate blood-meal analysis was successful in three samples sequenced, with mtDNA-based phylogenetic analyses revealing that blood-meal sources for Chrysops niger , Culex restuans and Aedes trivittatus were human, house sparrow ( Passer domesticus ) and eastern cottontail rabbit ( Sylvilagus floridanus ), respectively. Conclusions Our findings show that NAS has dual utility to simultaneously molecularly identify hematophagous insects and their blood-meal hosts. Moreover, our data indicate NAS can facilitate a wide array of mitogenomic systematic studies through novel ‘phylogenetic capture’ methods. We conclude that the NAS approach has great potential for broadly improving genomic resources used to identify blood-feeding insects, answer phylogenetic questions and elucidate complex pathways for the transmission of vector-borne pathogens. Graphical Abstract

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Adaptive sampling / Aedes - genetics / Aedes trivittatus / Aedes vexans / Analysis / Animals / Annotations / Aquatic insects / Arrays / Assembly / bioinformatics / Biomedical and Life Sciences / Biomedicine / Blood / blood meal / Chrysops / Chrysops niger / Culex - genetics / Culex restuans / Culex territans / Culicidae / Cytochrome / Deer / Disease / Disease transmission / DNA / DNA sequencing / DNA, Mitochondrial - genetics / Entomology / Experiments / Food and nutrition / Gene sequencing / Genes / Genetic aspects / Genetic research / genome assembly / Genome, Mitochondrial / Genomes / Genomics / hematophagous insects / hematophagy / Hosts / Humans / Identification / Infectious Diseases / Insects / Insects as carriers of disease / Laboratories / Linux / Mathematical analysis / Methods / MinION / Mitochondria / Mitochondrial DNA / mitochondrial genome / Mitochondrial genomes / Molecular barcoding / Mosquito Vectors / Mosquitoes / Nanopores / Nucleotide sequence / Nucleotide sequencing / Parasitology / Passer domesticus / Pathogens / Phylogenetic capture / Phylogenetics / Phylogeny / Rabbits / Risk factors / Sampling / Sequencing / species / statistical analysis / Streamlining / Sylvilagus floridanus / Tabanidae / Taxonomy / Tropical Medicine / Vector-borne diseases / Vectors / Vectors (Biology) / Vertebrates / Veterinary Medicine/Veterinary Science / Virology / Whole genome sequencing / Zoological research / Zoonoses