Ploidy variation and its implications for reproduction and population dynamics in two sympatric Hawaiian coral species

The response of coral reef ecosystems to anthropogenic climate change is driven by a complex interaction between location, stress history, species composition, and genetic background of the reef system. The latter two factors are particularly relevant when considering the different reproductive strategies used by coral species. We studied the stress resistant coral Montipora capitata and the more stress sensitive Pocillopora acuta from Kāneʻohe Bay, Oʻahu, Hawaiʻi. High-quality genome assemblies were generated for both species with the M. capitata assembly at chromosome-level resolution and the P. acuta assembly derived from a triploid colony, representing the first non-diploid genome generated from a coral. We report significant differences in the reproductive strategies of these coral species that not only affect the genetic structure of their populations in Kāneʻohe Bay, but also impact algal symbiont composition. Single-nucleotide polymorphism analysis shows that P. acuta comprises at least nine distinct genotypes in the bay with ancestral diploid and derived triploid lineages. In contrast, M. capitata colonies are diploids with nearly all being genotypically distinct. Genotype has a strong effect on gene expression profiles in these species, largely outweighing the effects of environmental stress. Our insights advance understanding of how reproductive strategy and ploidy can vary between different coral species and among local populations, how these factors constrain coral holobiont genetic diversity, and how genotype constrains genome-wide gene expression.