Current analysis of host–parasite interactions with a focus on next generation sequencing data

Abstract

Among the most common forms of interaction between species are those between hosts and their parasites and they have important implications for evolutionary theory. Understanding both the phenotypic and genotypic processes governing such interactions is a major endeavour in biology, but is a complex and challenging task. The development of next generation sequencing technologies has recently opened up this field from a molecular perspective, allowing us access to the genomic data underlying laboratory or wild phenotypes. The data obtained from such technologies has many advantages over previous methods, such as being more abundant, often more accurate, less labour intensive to generate and more cost effective to produce. We present a review of the impact of next generation sequencing data on the study of host-parasite evolution and current topics being explored with this data. We focus on two main data types, genomic and transcriptomic. We discuss popular computational approaches which can help us characterise the molecular forces driving host-parasite systems and highlight some studies which have utilised such approaches to gain information about particular immune processes. We furthermore highlight some promising perspectives from emerging and new technologies which will allow researchers to reach a deeper understanding of these interactions.

Dual transcriptomics reveals co‐evolutionary mechanisms of intestinal parasite infections in blue mussels Mytilus edulis

“…For example, chitin digestion of the hosts was coupled to cuticle protein expression in the parasite and might be a core mechanism underlying the resistance phenotype differences previously observed along the invasion fronts (Feis et al., ). Such coupled gene expression pattern not only demonstrates the usefulness of dual transcriptomics approaches (Greenwood et al., ), but, more importantly, it shows that regulation of functionally important differences evolved rapidly along the two invasion fronts, supporting the usefulness of invasive species’ natural history to understand host–parasite co‐evolution in the wild.…”

“…For example, chitin digestion of the hosts was coupled to cuticle protein expression in the parasite and might be a core mechanism underlying the resistance phenotype differences previously observed along the invasion fronts (Feis et al, 2016). Such coupled gene expression pattern not only demonstrates the usefulness of dual transcriptomics approaches (Greenwood et al, 2016), but, more importantly, it…”

“…Methodologically, macroparasite infections have the advantage that host and parasite transcriptomes can be sequenced separately, extending a dual transcriptomics approach to a dual‐species transcriptomics approach. In microbial infections, hosts and parasites often cannot be separated physically and classical dual transcriptomics relies on bioinformatic separation of host and parasite transcripts leading to heavy bias towards the host with only few parasite transcripts (Greenwood, Ezquerra, Behrens, Branca, & Mallet, ). Nevertheless, a dual transcriptomics approach can be very helpful to identify interacting genes (Schulze, Schleicher, Guthke, & Linde, ; Westermann, Gorski, & Vogel, ) and has been applied to several model organisms (e.g., Choi, Aliota, Mayhew, Erickson, & Christensen, ; Pittman, Aliota, & Knoll, ; Rosani et al., ; Tierney et al., ).…”

Tick-host-pathogen systems immunobiology an interactive trio

“…Accumulation of extensive molecular data sets underpins systems biology approaches to achieve genome-wide analyses of specific response networks, such as inflammation, in a variety of complex human diseases (160), veterinary infectious diseases (161) and host-parasite interactions (162,163). Current systems biology approaches depend upon recent major technological advances.…”

Rewilding and the risk of creating new, unwanted ecological interactions

“…For instance, an important aspect to take into account in rewilding programs is the maintenance or the possible disruption of existing biotic interactions, such as predatorprey or host-parasite relationships -or even both simultaneously, such as in predatorprey-parasite triangles (e.g., Barbosa et al 2012). Host-parasite interactions can have profound consequences on a variety of aspects, including population structure, social traits, physiology, macroecology and evolution (Guilhaumon et al 2012;Quingley et al 2012;Greenwood et al 2016). Predator-prey relationships also play a major role in the functioning of ecosystems.…”