Stony coral are a major keystone species for coral reef ecosystems. Although coral reefs cover 1% of the ocean floor, they are home to more than 25% of the ocean’s known biodiversity and provide habitat for many marine organisms .
Unfortunately, coral reefs are in decline in the U.S. and around the world. Increased ocean temperatures and changing ocean chemistry are the greatest global threats to coral reef ecosystems. These threats are caused by warmer atmospheric temperatures and increasing levels of carbon dioxide in seawater. Ecological stress brought on by changes in temperature, salinity, or acidification levels can break down the symbiotic relationship between reef-building coral and their intracellular photosynthetic dinoflagellates in a phenomenon known as bleaching .
Today, we highlight a chromosome-length genome assembly from our recent manuscript, for the species Acropora millepora, a scleractinian coral that inhabits coral reefs across the planet’s shallow ocean water. This chromosome-length assembly was generated via a Hi-C upgrade (using 3D-DNA and Juicer, see our Methods page for more details) of a draft genome assembly from (Ying et al., 2019). The A. millepora tissue used to generate the Hi-C data for the upgrade was obtained from a healthy coral identified by its skeletal morphology, particularly the arrangement of peripheral and axial coralites[DC1] . The sample was taken from a mature adult A. millepora that has established itself as a colony with a calcium carbonate skeleton.
To our knowledge, this is the first three-dimensional 3D-genome assembly of the A. millepora genome, and the first stony coral to have its genome three dimensionally mapped. A recently published excellent independent effort focusing on Genome Wide Association Studies (GWAS) of bleaching across 253 different coral larvae relied on a linkage map-based chromosome-level genome assembly . We hope that Hi-C data will not only help with improving the chromosome-length assembly for A. millepora and the associated downstream analyses, but also contribute to our understanding of the complex regulatory landscape associated with the complex phenomenon of bleaching, e.g., shed some light on the 3D arrangement of the locus encoding transcription of the heat-shock co-chaperone sacsin.