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Accepted (AM)Open Access (License Unspecified), Open
Journal article
Metatranscriptomics yields new genomic resources and sensitive detection of infections for diverse blood parasites
MOLECULAR ECOLOGY RESOURCES, v 20(1)
Jan 2020
PMID: 31507097
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Metatranscriptomics is a powerful method for studying the composition and function of complex microbial communities. The application of metatranscriptomics to multispecies 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 although they often occur at low infection intensities and exist as multispecies 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-sequencing of 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 of 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 similar to 23% more total parasite infections across all samples than were identified using microscopy and DNA barcoding. For single-species infections, we obtained data for >1,300 loci from samples with as low as 0.03% parasitaemia, 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.
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Details
- Title
- Metatranscriptomics yields new genomic resources and sensitive detection of infections for diverse blood parasites
- Publication Details
- MOLECULAR ECOLOGY RESOURCES, v 20(1)
- Publisher
- WILEY; HOBOKEN
- Number of pages
- 0
- Grant note
- American Museum of Natural History; National Institutes of Health, Grant/Award Number: 1R03AI117223-01A1; Division of Biological Infrastructure, Grant/Award Number: 1811806; Federal Bureau of Land Management Rio Puerco Field Office; New Mexico Ornithological Society; Richard Gilder Graduate Scool; Society of Systematic Biologists; Explorers Club
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Drexel University
- Web of Science ID
- WOS:000502400500001
- Scopus ID
- 2-s2.0-85076351833
- Other Identifier
- 991021860673104721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biochemistry & Molecular Biology
- Ecology
- Evolutionary Biology