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Long-read sequencing is revolutionizingde-novogenome assemblies, with continued advancements making it more readily available for previously understudied, non-model organisms. Stony corals are one such example, with long-readde-novogenome assemblies now starting to be publicly available, opening the door for a wide array of ‘omics-based research. Here we present a newde-novogenome assembly for the endangered Caribbean star coral,Orbicella faveolata, using PacBio circular consensus reads. Our genome assembly improved the contiguity (51 versus 1,933 contigs) and complete and single copy BUSCO orthologs (93.6% versus 85.3%, database metazoa_odb10), compared to the currently available reference genome generated using short-read methodologies. Our newde-novoassembled genome also showed comparable quality metrics to other coral long-read genomes. Telomeric repeat analysis identified putative chromosomes in our scaffolded assembly, with these repeats at either one, or both ends, of scaffolded contigs. We identified 32,172 protein coding genes in our assembly through use of long-read RNA sequencing (ISO-seq) of additionalO. faveolatafragments exposed to a range of abiotic and biotic treatments, and publicly available short-read RNA-seq data. With anthropogenic influences heavily affectingO. faveolata, as well as itsincreasing incorporation into reef restoration activities, this updated genome resource can be used for population genomics and other ‘omics analyses to aid in the conservation of this species.

 

The rapid loss of reef-building corals owing to ocean warming is driving the development of interventions such as coral propagation and restoration, selective breeding and assisted gene flow. Many of these interventions target naturally heat-tolerant individuals to boost climate resilience, but the challenges of quickly and reliably quantifying heat tolerance and identifying thermotolerant individuals have hampered implementation. Here, we used coral bleaching automated stress systems to perform rapid, standardized heat tolerance assays on 229 colonies of Acropora cervicornis across six coral nurseries spanning Florida's Coral Reef, USA. Analysis of heat stress dose–response curves for each colony revealed a broad range in thermal tolerance among individuals (approx. 2.5°C range in F v /F m ED50), with highly reproducible rankings across independent tests ( r = 0.76). Most phenotypic variation occurred within nurseries rather than between them, pointing to a potentially dominant role of fixed genetic effects in setting thermal tolerance and widespread distribution of tolerant individuals throughout the population. The identification of tolerant individuals provides immediately actionable information to optimize nursery and restoration programmes for Florida's threatened staghorn corals. This work further provides a blueprint for future efforts to identify and source thermally tolerant corals for conservation interventions worldwide. 

The carbon isotope fractionation in algal organic matter (ε_p), including the long‐chain alkenones produced by the coccolithophorid family Noelaerhabdaceae, is used to reconstruct past atmospheric CO₂levels. The conventional proxy linearly relates ε_pto changes in cellular carbon demand relative to diffusive CO₂supply, with larger ε_pvalues occurring at lower carbon demand relative to supply (i.e., abundant CO₂). However, the response ofGephyrocapsa oceanica, one of the dominant alkenone producers of the last few million years, has not been studied closely. Here, we subjectG. oceanicato various CO₂levels by increasing pCO₂in the culture headspace, as opposed to increasing dissolved inorganic carbon (DIC) and alkalinity concentrations at constant pH. We note no substantial change in physiology, but observe an increase in ε_pas carbon demand relative to supply decreases, consistent with DIC manipulations. We compile existing Noelaerhabdaceae ε_pdata and show that the diffusive model poorly describes the data. A meta‐analysis of individual treatments (unique combinations of lab, strain, and light conditions) shows that the slope of the ε_presponse depends on the light conditions and range of carbon demand relative to CO₂supply in the treatment, which is incompatible with the diffusive model. We model ε_pas a multilinear function of key physiological and environmental variables and find that both photoperiod duration and light intensity are critical parameters, in addition to CO₂and cell size. While alkenone carbon isotope ratios indeed record CO₂information, irradiance and other factors are also necessary to properly describe alkenone ε_p.