Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

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

Näpflin, Kathrin ; Becks, Lutz ; Bensch, Staffan LU orcid ; Ellis, Vincenzo LU ; Hafer-Hahmann, Nina ; Harding, Karin ; Lindén, Sara ; O'Connor, Emily LU orcid ; Olsen, Morten and Roved, Jacob LU , et al. (2019) In PeerJ Preprints
Abstract
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... (More)
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. (Less)
Please use this url to cite or link to this publication:
author
; ; ; ; ; ; ; ; and , et al. (More)
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; and (Less)
organization
publishing date
type
Contribution to journal
publication status
submitted
subject
keywords
Plasmodium, MHC, immunotoxins, mucus, natural selection, GWAS, infectious diseases, anthropogenic stressors, co-evolution, epidemiological surveillance
in
PeerJ Preprints
article number
7:e27734v1
ISSN
2167-9843
DOI
10.7287/peerj.preprints.27734v1
language
English
LU publication?
yes
id
7fbc1703-2721-4dda-b677-d7d922b14d33
date added to LUP
2019-10-17 11:04:31
date last changed
2021-01-05 16:07:41
@article{7fbc1703-2721-4dda-b677-d7d922b14d33,
  abstract     = {{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.}},
  author       = {{Näpflin, Kathrin and Becks, Lutz and Bensch, Staffan and Ellis, Vincenzo and Hafer-Hahmann, Nina and Harding, Karin and Lindén, Sara and O'Connor, Emily and Olsen, Morten and Roved, Jacob and Sackton, Timothy and Shultz, Allison and Venkatakrishnan, Vignesh and Videvall, Elin and Westerdahl, Helena and Winternitz, Jamie and Edwards, Scott}},
  issn         = {{2167-9843}},
  keywords     = {{Plasmodium, MHC, immunotoxins, mucus, natural selection, GWAS, infectious diseases, anthropogenic stressors, co-evolution, epidemiological surveillance}},
  language     = {{eng}},
  series       = {{PeerJ Preprints}},
  title        = {{Genomics of host-pathogen interactions : challenges and opportunities across ecological and spatiotemporal scales}},
  url          = {{http://dx.doi.org/10.7287/peerj.preprints.27734v1}},
  doi          = {{10.7287/peerj.preprints.27734v1}},
  year         = {{2019}},
}