Toward the generation of pure coral genomes with experimental and bioinformatic improvements

The advancement of genomics technology has revolutionized research on diverse taxa, significantly improving our understanding of species biology and evolution. Genome sequencing is the initial step required for comprehensive representation of a species’ genome and provides reference data for further analyses. The genomes of numerous marine species remain unexamined, because either their importance is overlooked or there are significant challenges associated with acquiring biological samples.1 Stony corals are foundational reef builders that house one-third of marine biodiversity and act as an important carbon sink, making them essential for marine conservation and sustainable development.2,3 They have a symbiotic relationship with single-celled algae (Symbiodiniaceae) that reside within coral symbiotic cells. These algae supply corals with energy through photosynthesis and underpin the growth and development of coral reefs.

However, these endosymbiotic partners pose a challenge to genomic research because their DNA is often coextracted with coral DNA, leading to contamination and assembly errors. Additionally, the presence of microorganisms and invertebrates within the porous structure of coral skeletons further complicates the extraction of the DNA composition of stony coral samples. Failure to detect nontarget sequences from associated organisms in the genome assembly and the lack of reliable coral genomic resources may result in spurious interpretation of species evolutionary history and metabolic potential. This can obstruct our understanding of coral adaptation, evolution, and response to environmental changes, leading to missed opportunities for biotechnology applications and targeted conservation strategies.