Montagem do genoma de Madrepora oculata (Cnidaria, Scleractinia)

Abstract

Deep-sea scleractinian corals play a crucial role in maintaining marine biodiversity and regulating ocean biogeochemical processes. Among them, Madrepora oculata stands out as an important reef-building species with a broad geographic distribution. High-quality genome assemblies are essential for evolutionary, ecological, and adaptive studies; however, genomic resources for deep-sea corals remain scarce. In this context, the present study aimed to assemble the nuclear and mitochondrial genomes of M. oculata using Illumina short-read and Oxford Nanopore long-read sequencing data. Specimens were collected at a depth of 663 m in the Bacia de Campos and preserved frozen for subsequent DNA extraction and sequencing. Taxonomic identity was first confirmed through phylogenetic analyses based on ultraconserved elements (UCEs). Nuclear genome assembly was performed using long-read sequencing data, followed by polishing with short reads. Assembly quality was assessed before and after polishing, and genome size, heterozygosity, and repetitive content were estimated. Finally, the mitochondrial genome was assembled and annotated. Phylogenetic analyses confirmed the specimen as M. oculata rather than the cryptic species M. piresae. K-mer distribution analysis estimated a haploid genome size of approximately 447 Mb, with a heterozygosity rate of 0.88% and 56.1% unique sequences. This estimate contrasted with the final nuclear assembly size of approximately 675 Mb, likely due to the retention of heterozygous loci as separate sequences. Despite the observed fragmentation, evidenced by 5,040 contigs and an N50 of 233.5 kb, the assembly achieved 94.4% BUSCO completeness, indicating successful recovery of most essential gene content and yielding values comparable to those reported for recently published scleractinian coral genomes. The mitochondrial genome showed an average coverage of 10,751× and was recovered as a single circular contig of 15,804 bp. The assembled sequence differed from the previously published reference mitogenome by only 37 bp, primarily within an intergenic region between the cox2 and cox3 genes, a variation that has also been observed in other Atlantic specimens. This study represents one of the first efforts to generate a nuclear genome assembly for a deep-sea scleractinian coral and provides valuable genomic resources for future evolutionary, phylogenomic, and functional investigations.