MITOGENOME STABILITY AND STRUCTURAL VARIATION IN ACROPORA DIGITIFERA: A COMPARATIVE GENOMIC AND ANNOTATION-INTEGRATED ASSESSMENT

Abstract

Understanding mitochondrial genome evolution is crucial for resolving phylogenetic relationships and assessing genomic stability across reef-building corals. In this study, we systematically examined the mitochondrial genomes of five Acropora digitifera samples (S1B–S5A) collected from the coastal waters of Oman to investigate patterns of gene order conservation, strand orientation, and structural variation. Using annotation-informed genome visualization tools, including circular genome maps and gene order dot plots, we revealed highly conserved mitochondrial architecture among samples, with minor sample-specific deviations such as split rrnS annotations in S3A and duplicated replication origin regions (OH_2) in S2D.

Protein-coding genes (PCGs) and transfer RNA genes were predominantly located on the positive strand, while ribosomal RNA genes (rrnL, rrnS) and trnM(cat) were consistently encoded on the negative strand across all samples. BUSCO analysis of corresponding nuclear genome assemblies showed strong correlation with mitochondrial genome quality, with completeness scores ranging from 25.5% (S4A) to 53.7% (S5A), indicating that structural anomalies were more prevalent in assemblies with lower overall genome completeness.

Comparative analysis with published coral mitogenomes confirmed both the overall stability and minor plasticity of organellar genomes in A. digitifera. This study highlights the importance of high-quality genome assembly and annotation tools for reliable mitochondrial genome interpretation, and provides a valuable framework for future phylogenomic and population genomic research in scleractinian corals. Our findings contribute to understanding mitochondrial evolution in reef-building corals and establish baseline genomic resources for the understudied coral fauna of the Arabian Sea and Gulf of Oman.