Genomics of hosts-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales
- Published
- Accepted
- Subject Areas
- Biodiversity, Ecology, Evolutionary Studies, Genomics, Zoology
- Keywords
- Plasmodium, MHC, immunotoxins, mucus, natural selection, GWAS, infectious diseases, anthropogenic stressors, co-evolution, epidemiological surveillance
- Copyright
- © 2019 Näpflin et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2019. Genomics of hosts-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales. PeerJ Preprints 7:e27734v1 https://doi.org/10.7287/peerj.preprints.27734v1
Abstract
Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed to the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
SI Table 1: References and scoring results of literature survey
Literature search on Web of Science (accessed August 30, 2018) with the following search query: (host-parasite* OR host-pathogen*) AND (genomic*). We refined the search hits by document type to include only articles, covering the publication years 2014-2018, and excluding studies with no genomic aspect. The table contains 263 papers with scores for each scale defined in Table 1.