Data from: Metatranscriptomics yields new genomic resources and sensitive detection of infections for diverse blood parasites

Metatranscriptomics is a powerful method for studying the composition and
function of complex microbial communities. The application of
metatranscriptomics to multi-species parasite infections is of particular
interest, as research on parasite evolution and diversification has been
hampered by technical challenges to genome-scale DNA sequencing. In
particular, blood parasites of vertebrates are abundant and diverse though
they often occur at low infection intensities and exist as multi-species
infections, rendering the isolation of genomic sequence data challenging.
Here, we use birds and their diverse haemosporidian parasites to
illustrate the potential for metatranscriptome sequencing to generate
large quantities of genome-wide sequence data from multiple blood parasite
species simultaneously. We used RNA-Seq on 24 blood samples from songbirds
in North America to show that metatranscriptomes can yield large
proportions of haemosporidian protein-coding gene repertoires even when
infections are low-intensity (<0.1% red blood cells infected) and
consist of multiple parasite taxa. By bioinformatically separating host
and parasite transcripts and assigning them to the haemosporidian genus of
origin, we found that transcriptomes detected ~23% more total parasite
infections across all samples than were identified using microscopy and
DNA barcoding. For single-species infections, we obtained data for upwards
of 1,300 loci from samples with as low as 0.03% parasitemia, with the
number of loci increasing with infection intensity. In total, we provide
data for 1,502 single-copy orthologous loci from a
phylogenetically-diverse set of 33 haemosporidian mitochondrial lineages.
The metatranscriptomic approach described here has the potential to
accelerate ecological and evolutionary research on haemosporidians and
other diverse parasites.