Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus.

Abstract

Background: Corals are capable of launching diverse immune defenses at the site of direct contact with pathogens, but the molecular mechanisms of this activity and the colony-wide effects of such stressors remain poorly understood. Here we compared gene expression profiles in eight healthy Acropora hyacinthus colonies against eight colonies exhibiting tissue loss commonly associated with white syndromes, all collected from a natural reef environment near Palau. Two types of tissues were sampled from diseased corals: visibly affected and apparently healthy. Results: Tag-based RNA-Seq followed by weighted gene co-expression network analysis identified groups of co-regulated differentially expressed genes between all health states (disease lesion, apparently healthy tissues of diseased colonies, and fully healthy). Differences between healthy and diseased tissues indicate activation of several innate immunity and tissue repair pathways accompanied by reduced calcification and the switch towards metabolic reliance on stored lipids. Unaffected parts of diseased colonies, although displaying a trend towards these changes, were not significantly different from fully healthy samples. Still, network analysis identified a group of genes, suggestive of altered immunity state, that were specifically up-regulated in unaffected parts of diseased colonies. Conclusions: Similarity of fully healthy samples to apparently healthy parts of diseased colonies indicates that systemic effects of white syndromes on A. hyacinthus are weak, which implies that the coral colony is largely able to sustain its physiological performance despite disease. The genes specifically up-regulated in unaffected parts of diseased colonies, instead of being the consequence of disease, might be related to the originally higher susceptibility of these colonies to naturally occurring white syndromes.

Gene expression stasis and plasticity following migration into a foreign environment

“…GO enrichment was conducted according to Wright et al. () using transcriptome annotation built with the uniprotkb database and following previously described procedures (Dixon et al., ; Lohman, Steinel, Weber, & Bolnick, In review).…”

“…TagSeq libraries were sequenced on the HiSeq 2500 with 1x100V4 chemistry at the Genome Sequencing and Analysis Facility at the University of Texas at Austin, generating an average of~5 M raw reads per sample. This read depth is appropriate for TagSeq (because sequencing effort is targeted at the 3 0 end of the mRNA) and has been shown to be successful (Dixon et al, 2015;Kenkel & Matz, 2016;Lohman et al, 2016;Meyer, Aglyamova, & Matz, 2011;Meyer et al, 2009;Wright, Aglyamova, Meyer, & Matz, 2015).…”

Free‐living and symbiotic lifestyles of a thermotolerant coral endosymbiont display profoundly distinct transcriptomes under both stable and heat stress conditions

“…Following transcript quantification with Salmon (Patro, Duggal, Love, Irizarry, & Kingsford, 2017), differential gene expression analysis was performed in edger (Robinson, McCarthy, & Smyth, 2010) using a generalized linear model to determine the effects of temperature and symbiotic state as well as the interaction between the two on changes in transcript expression. Log 2 fold change values for all transcripts were subject to gene ontology (GO) enrichment analyses within the r package GO_MWU (Wright, Aglyamova, Meyer, & Matz, 2015).…”

Molecular mechanisms of acclimation to long‐term elevated temperature exposure in marine symbioses

“…The downstream, module‐wise GO enrichment analyses followed the pipeline outlined above. Finally, we used the “ GO_deltaRanks_correlation ” function implemented in the GO_MWU R package (Wright et al, ) to assess similarity between response to stress in symbiont in hospite with clams in and specific mechanisms of thermotolerance for cultured Symbiodiniaceae.…”