Chromosome-level genomes of scleractinian corals: gene prediction and functional annotation

Overview

Scleractinia (stony corals) are a diverse taxonomic order within the phylum Cnidaria, comprising more than 1,600 species described to date. Most of these corals play a key role as reef builders by secreting calcium carbonate, forming rigid skeletons that provide the structural foundation of tropical coral reef ecosystems. Through colonial growth and symbioses with their photosynthetic microalgae (Symbiodiniaceae) and a suite of other microorganisms, scleractinian corals support high primary productivity and underpin the vast biodiversity of coral reefs. Corals are under severe pressure from climate change, including ocean warming and acidification, which threaten their survival and, consequently, the persistence of coral reef systems globally. In recent years, significant efforts have been made to increase the number of sequenced genomes from scleractinian corals, thereby providing crucial insights into their biology, evolution, resilience, and vulnerability. However, there are few high-quality reference genomes for Scleractinia, and many available genomes remain unannotated, creating barriers to collaboration and scientific insight. Annotation outcomes also vary depending on the methods and software utilised. To address these issues, we applied a standardised pipeline for generating high-quality gene models to 40 scleractinian genomes, spanning 22 genera across 13 families. These genomes, produced through the Aquatic Symbiosis Genomics (ASG) Project, are publicly available. This curated resource of annotated quality genomes will provide essential molecular tools at a critical time for coral reef conservation. 

Contributors

Sebastian Metz [1], Michael Paulini [2], Kara Rising [1], Kate M. Quigley [3,4,5], Christian R Voolstra [6], David J. Combosch [7], Maren Ziegler [8], John Everett Parkinson [9], Victoria McKenna [2], Rebecca O'Brien [2], Haoyu Niu [2], Alice Linsdell [2], Eerik Aunin [2], Noah Gettle [2], Graeme Oatley [2], Radka Platte [2], Jonathan Wood [2], Shane McCarthy [2], Nancy Holroyd [2], Caroline Howard [2], Jim Downie [2], Camilla Santos [2], Wiesia Johnson [2], Elizabeth Sinclair [2], Joanna Collins [2], Sarah Pelan [2], Danil Zilov [2], Karen Brooks [2], Karen van Niekerk [2], Dominic Absolon [2], Thomas C. Mathers [2], Benjamin Jackson [2], Kerstin Howe [2], Mark Blaxter [2], Michael Sweet [1]

Affiliations

[1]: Aquatic Research Facility, Nature-based Solutions Research Centre, University of Derby, Derby, UK

[2]: Wellcome Sanger Institute, Cambridge, UK

[3]: Minderoo Foundation, Perth, Western Australia, Australia

[4]: James Cook University, Townsville, Queensland, Australia

[5]: University of Western Australia, Perth, Western Australia, Australia

[6]: University of Konstanz, Konstanz, Germany

[7]: University of Guam, Guam, USA

[8]: Justus Liebig University Giessen, Giessen, Germany

[9]: University of South Florida, Tampa, Florida, USA