Re-annotation improved large-scale assembly of the reef-building coral Acropora intermedia.

Acropora corals, primary reef-builders providing habitat for numerous marine species, now face novel survival pressures due to environmental changes. Acropora intermedia (Brook 1891), a significant contributor to the vibrant ecosystems of coral reefs in the Indo-Pacific Ocean, also exhibits enhanced resistance to both thermal and acid stress. To advance future studies, we report an improved high-quality genome assembly for A. intermedia obtained through PacBio Hi-Fi long-read sequencing, with a total size of 496.8 Mb. Compared to the previous version, our genome assembly shows substantial improvements in contiguity, with the Contig N50 increasing from 40.3 Kb to 2.9 Mb, and the number of contigs decreasing from 20,998 to 633. Specifically, our genome exhibits no undetectable ambiguous bases (N's) per 100 Kbp, which is remarkably lower than the previous version (5,276.11 per 100 Kbp). The percentage of assembly completeness evaluation based on Benchmarking Universal Single-Copy Orthologs (BUSCO) has increased from 90.6% to 92.6%. We predict a total of 26,852 protein-coding genes, with a BUSCO completeness of 95.7%, marking a 2.7% increase from the previous assembly. Our re-annotation and improved genome assembly of A. intermedia provide a valuable resource for further studies on coral adaptation mechanisms under climate change, and will facilitate comparative and evolutionary research of Acropora.