Genomic basis for coral resilience to climate change

Abstract

Recent advances in DNA-sequencing technologies now allow for in-depth characterization of the genomic stress responses of many organisms beyond model taxa. They are especially appropriate for organisms such as reef-building corals, for which dramatic declines in abundance are expected to worsen as anthropogenic climate change intensifies. Different corals differ substantially in physiological resilience to environmental stress, but the molecular mechanisms behind enhanced coral resilience remain unclear. Here, we compare transcriptome-wide gene expression (via RNA-Seq using Illumina sequencing) among conspecific thermally sensitive and thermally resilient corals to identify the molecular pathways contributing to coral resilience. Under simulated bleaching stress, sensitive and resilient corals change expression of hundreds of genes, but the resilient corals had higher expression under control conditions across 60 of these genes. These “frontloaded” transcripts were less up-regulated in resilient corals during heat stress and included thermal tolerance genes such as heat shock proteins and antioxidant enzymes, as well as a broad array of genes involved in apoptosis regulation, tumor suppression, innate immune response, and cell adhesion. We propose that constitutive frontloading enables an individual to maintain physiological resilience during frequently encountered environmental stress, an idea that has strong parallels in model systems such as yeast. Our study provides broad insight into the fundamental cellular processes responsible for enhanced stress tolerances that may enable some organisms to better persist into the future in an era of global climate change.

Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2‐acidified sea water

“…Combined with a good BUSCO completeness measure, this indicates that our transcriptome is of high quality. While ~0.25% of the transcriptome significantly differentially expressed is a low percentage, it is similar to other studies using nontargeted investigations of the entire transcriptome: in a copepod in response to heat stress (0.88%; Schoville, Barreto, Moy, Wolff, & Burton, 2012), an Antarctic fish in response to pH and heat stress (0.08%–1.0%; Huth & Place, 2016), corals in response to heat stress (0.4%–0.7%; Barshis et al., 2013), and sea grass in response to heat stress (0.8%; Franssen et al., 2011). However, other studies have found greater percentages of the transcriptome affected (e.g., corals in response to low pH; 12%–19%; Moya, Huisman, & Ball, 2012; or heat shock; 27%; Seneca & Palumbi, 2015).…”

“…With six measurements at each pH (five in the pH 7.95 treatment) and samples consisting of pooled individuals, we were able to conservatively select only the consistent signals in gene expression (Schurch et al., 2016). Furthermore, few papers examine differential gene expression over >2 pH treatments or use pH as a continuous variable (i.e., Barshis et al., 2013; Seneca & Palumbi, 2015; Huth & Place, 2016). By treating pH as a continuous variable (as opposed to a factor) and collecting data from four pHs, we narrowed the focus of this study to genes differentially expressed consistently over the investigated pH range, rather than those reacting to specific treatments, and reduced the chance of false positives.…”

Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata

“…Both bacterial and Symbiodinium community composition have been assessed in some coral diseases (Cervino et al, 2004). However, the host physiological response has been evaluated mainly in the context of thermal stress (DeSalvo et al, 2008;Barshis et al, 2013) and never in conjunction with microbial community profiling. Host transcriptome profiling can enhance our understanding of how corals are responding to disease outbreak.…”

“…16S ribosomal RNA gene microarrays, known as 'PhyloChips', provide a culture independent method to monitor relative abundance of a set of bacterial taxa under different conditions (Brodie et al, 2006), and have been extensively used in different biological systems (Wu et al, 2010;Mendes et al, 2011), including corals Kellogg et al, 2012;Roder et al, 2014). Coral transcriptome profiling has been used to examine differential gene expression under multiple physiological and developmental conditions (DeSalvo et al, 2008;Voolstra et al, 2009a,b;Portune et al, 2010;Bellantuono et al, 2012;Kaniewska et al, 2012;Barshis et al, 2013). Herein we extend the use coral complimentary DNA (cDNA) microarrays to examine host response to disease.…”

Climate-change adaptation: Designer reefs

“…In a study 6 published in 2013, Palumbi and his colleagues, including Daniel Barshis, a marine biologist at Stanford, compared two populations of the reef-building coral Acropora hyacinthus at their field site off Ofu Island in American Samoa. One population lives in the toasty pool where temperatures reach 35 °C during summer low tides and fluctuate by up to 6 °C daily; the other, less isolated by tides, has to deal with temperatures of only about 29 °C.…”