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Genomics of host-pathogen interactions : challenges and opportunities across ecological and spatiotemporal scales

Author:
  • Kathrin Näpflin
  • Lutz Becks
  • Staffan Bensch
  • Vincenzo Ellis
  • Nina Hafer-Hahmann
  • Karin Harding
  • Sara Lindén
  • Emily O'Connor
  • Morten Olsen
  • Jacob Roved
  • Timothy Sackton
  • Allison Shultz
  • Vignesh Venkatakrishnan
  • Elin Videvall
  • Helena Westerdahl
  • Jamie Winternitz
  • Scott Edwards
Publishing year: 2019
Language: English
Publication/Series: PeerJ Preprints
Document type: Journal article

Abstract english

Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed 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.

Keywords

  • Bioinformatics and Systems Biology
  • Evolutionary Biology
  • Genetics
  • Plasmodium, MHC, immunotoxins, mucus, natural selection, GWAS, infectious diseases, anthropogenic stressors, co-evolution, epidemiological surveillance

Other

Submitted
  • ISSN: 2167-9843
Staffan Bensch
E-mail: staffan [dot] bensch [at] biol [dot] lu [dot] se

Professor

MEMEG

+46 46 222 42 92

E-C213

Sölvegatan 37, Lund

50

Head of unit

MEMEG

+46 46 222 42 92

E-C213

Sölvegatan 37, Lund

50

Research group

Molecular Ecology and Evolution Lab

Projects

Doctoral students and postdocs

PhD students, main supervisor

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