Genome assembly and annotation of Acropora pulchra from Mo'orea French Polynesia

Abstract

Reef-building corals are integral ecosystem engineers of tropical reefs but face threats from climate change. Investigating genetic, epigenetic, and environmental factors influencing their adaptation is critical. Genomic resources are essential for understanding coral biology and guiding conservation efforts. However, genomes of the coral genus Acropora are limited to highly-studied species. Here, we present the assembly and annotation of the genome and DNA methylome of Acropora pulchra from Mo'orea, French Polynesia. Using long-read PacBio HiFi and Illumina RNASeq, we generated the most complete Acropora genome to date (BUSCO completeness of 96.7% metazoan genes). The assembly size is 518 Mbp, with 174 scaffolds, and a scaffold N50 of 17 Mbp. We predicted 40,518 protein-coding genes and 16.74% of the genome in repeats. DNA methylation in the CpG context is 14.6%. This assembly of the A. pulchra genome and DNA methylome will support studies of coastal corals in French Polynesia, aiding conservation and comparative studies of Acropora and cnidarians.

Figure 1.

Image of Study Species and Geographic Distribution. (a) Images of Acropora pulchra in Mo’orea taken by Trinity Conn. (b) Map of the distribution of Acropora pulchra in the tropical pacific from the Coral Trait Database, edited by Joshua Madin, species ID 145 [5].

Figure 2.

(a) K-mer multiplicity plot and estimates of genome size and heterozygosity as inferred by GenomeScope2.0. (b) Final assembly of the circularized mitochondrial genome. Genic regions in red are tRNA-protein coding genes. Genic regions in orange are COX genes. Genic regions in purple are genes related to the production of NADH dehydrogenase. Genic regions in blue are genes related to the production of ATP synthase. Genic regions in dark green produce cytochrome B. Genic regions in light green are genes involved in the generation of ribosomal RNAs. Mitochondria were circularized starting with tRNAGly.

Figure 3.

Snail plot of Statistics Across the Final Masked Genome. Nucleotide composition presented in dark (GC content) and light (AT content) blue. GC content was consistent across the entire genome at approximately 39.1%. Scaffold length statistics are presented in orange, red, and grey.

Figure 4.

(a) Distribution of CpG sites across genomic features. (b) Percentage of CpGs methylated, partially methylated, and unmethylated in exons, introns, and intergenic regions. (c) Distribution of CpGs and their methylation probability across the first 100,000 bp of the ten longest scaffolds in the Acropora pulchra genome. Purple sections are exons, orange sections are introns, and gray sections are intergenic regions. The scaffold name is to the left of each scaffold. Each point represents a CpG location. The color and height (0 to 1) of the point on the y-axis represent the probability that the specific CpG site is methylated. Red indicates a higher probability of methylation, and blue indicates a lower probability of methylation.

Figure 5.

BUSCO Completeness of 954 conserved metazoan orthologs across Acropora Genome Assemblies. See Table 1 for the citations of each genome. The genome of Acropora pulchra presented in this paper represents the most complete Acroporid genome to date, with 95.1% complete and single-copy BUSCOs, 1.6% complete and duplicated BUSCOs, 0.9% fragmented, and 2.4% missing.