Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales
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 dyna...
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PeerJ Inc.
2019-11-01
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Series: | PeerJ |
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Online Access: | https://peerj.com/articles/8013.pdf |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Kathrin Näpflin Emily A. O’Connor Lutz Becks Staffan Bensch Vincenzo A. Ellis Nina Hafer-Hahmann Karin C. Harding Sara K. Lindén Morten T. Olsen Jacob Roved Timothy B. Sackton Allison J. Shultz Vignesh Venkatakrishnan Elin Videvall Helena Westerdahl Jamie C. Winternitz Scott V. Edwards |
spellingShingle |
Kathrin Näpflin Emily A. O’Connor Lutz Becks Staffan Bensch Vincenzo A. Ellis Nina Hafer-Hahmann Karin C. Harding Sara K. Lindén Morten T. Olsen Jacob Roved Timothy B. Sackton Allison J. Shultz Vignesh Venkatakrishnan Elin Videvall Helena Westerdahl Jamie C. Winternitz Scott V. Edwards Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales PeerJ Plasmodium MHC Immunotoxins Mucus Natural selection GWAS |
author_facet |
Kathrin Näpflin Emily A. O’Connor Lutz Becks Staffan Bensch Vincenzo A. Ellis Nina Hafer-Hahmann Karin C. Harding Sara K. Lindén Morten T. Olsen Jacob Roved Timothy B. Sackton Allison J. Shultz Vignesh Venkatakrishnan Elin Videvall Helena Westerdahl Jamie C. Winternitz Scott V. Edwards |
author_sort |
Kathrin Näpflin |
title |
Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales |
title_short |
Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales |
title_full |
Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales |
title_fullStr |
Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales |
title_full_unstemmed |
Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales |
title_sort |
genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales |
publisher |
PeerJ Inc. |
series |
PeerJ |
issn |
2167-8359 |
publishDate |
2019-11-01 |
description |
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. |
topic |
Plasmodium MHC Immunotoxins Mucus Natural selection GWAS |
url |
https://peerj.com/articles/8013.pdf |
work_keys_str_mv |
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doaj-be3974b735454baa914bdd4b8ae3d6742020-11-25T02:01:42ZengPeerJ Inc.PeerJ2167-83592019-11-017e801310.7717/peerj.8013Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scalesKathrin Näpflin0Emily A. O’Connor1Lutz Becks2Staffan Bensch3Vincenzo A. Ellis4Nina Hafer-Hahmann5Karin C. Harding6Sara K. Lindén7Morten T. Olsen8Jacob Roved9Timothy B. Sackton10Allison J. Shultz11Vignesh Venkatakrishnan12Elin Videvall13Helena Westerdahl14Jamie C. Winternitz15Scott V. Edwards16Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of AmericaMolecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, SwedenAquatic Ecology and Evolution, Limnological Institute University Konstanz, Konstanz, GermanyMolecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, SwedenMolecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, SwedenDepartment of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, GermanyDepartment of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, SwedenDepartment of Medical Chemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, SwedenSection for Evolutionary Genomics, Natural History Museum of Denmark, Department of Biology, University of Copenhagen, Copenhagen, DenmarkMolecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, SwedenInformatics Group, Harvard University, Cambridge, MA, United States of AmericaOrnithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA, United States of AmericaDepartment of Medical Chemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, SwedenMolecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, SwedenMolecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, SwedenDepartment of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, GermanyDepartment of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of AmericaEvolutionary 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.https://peerj.com/articles/8013.pdfPlasmodiumMHCImmunotoxinsMucusNatural selectionGWAS |