Data from: Going mobile: Using portable genomic technologies for PCR-free in situ species identification and real-time molecular systematics

Across the globe, anthropogenic environmental changes are threatening
animal biodiversity and contributing to the emergence of vector-borne and
zoonotic pathogens through host range shifts. To combat these challenges,
accurate and timely biodiversity assessments and molecular species
monitoring efforts are critical. Here, we document how implementation of a
portable laboratory in combination with targeted long-read nanopore
sequencing can facilitate in situ genomic and systematic analyses across
several animal taxa. Working at two ecologically divergent field sites in
Guyana, South America, we collected small mammals and blood-feeding
insects, including bats, rodents, a marsupial, mosquitoes, and a
phlebotomine sand fly. For each specimen sampled, genomic DNA was
extracted in the field and used for preparation of nanopore sequencing
libraries. For field sequencing, we utilized a novel software-based
targeted sequencing approach—nanopore adaptive sampling (NAS)—that enabled
selective sequencing of mitochondrial reads using mitogenome assemblies of
related taxa as enrichment targets. Basecalled reads from our field
sequencing experiments were used to assemble complete mitogenomes and to
generate mitochondrial biomarker consensus gene sequences for all nine
small mammals and four blood-feeding insects sequenced. Confirmatory
molecular identifications were made with a combination of local nucleotide
BLAST queries and maximum likelihood analyses using biomarker consensus
sequences. Importantly, the mitogenome-based targeted sequencing
strategies outlined here are amplification-free and allowed us to bypass
time-consuming and potentially troublesome PCR-based methods in the field,
streamlining library preparation, sequencing experiments, and on-site
analyses. Our findings describe targeted sequencing with NAS as an
effective tool for implementation into portable laboratories to widely
enhance field-based biodiversity monitoring and rapid molecular species
assessments across vertebrate and invertebrate hosts of consequential
emerging pathogens.