The complete mitochondrial genome of the ‘maze’ coral <i>Meandrina meandrites</i> (Scleractinia: Vacatina: Meandrinidae)

The shallow water reef-building 'maze' or 'brain' stony coral <i>Meandrina meandrites</i> (fam. Meandrinidae) is currently experiencing major environmental problems in the Caribbean Sea. In this study, we assembled the mitochondrial genome of <i>M. meandrites</i> to support future conservation of this imperiled coral. We also explored the phylogenetic position of this coral in the Class Scleractinia utilizing the phylogenetic signal provided by translated mitochondrial protein-coding genes (PCGs). A complete mitochondrial genome of <i>M. meandrites</i>, 17,196 bp in length, was assembled using short-reads next-generation sequencing (NGS) sequencing with the target-restricted-assembly pipeline GetOrganelle. The newly assembled mitochondrial genome of <i>M. meandrites</i> encoded 13 PCGs, two ribosomal genes (ribosomal RNA), and two transfer genes (tRNAs). It also contains two relatively long non-coding regions 400 and 1,877 bp long. A group I intron bisected the <i>nad5</i> PCG. Each of the two tRNAs exhibited a canonical 'cloverleaf' secondary structure. The mitochondrial genome of <i>M. meandrites</i> is identical to that of a conspecific assembled using HiFi PacBio long reads (available in GenBank with accession number OY855917 but without a companion paper) with the exception of four single nucleotide variants. The aforementioned comparison indicates that the mitochondrial genome assembled from a short-read NGS dataset is reliable (complete and accurate). A maximum-likelihood phylomitogenomic analysis based on PCGs (translated) supported the monophyly of the order Scleractinia and placed <i>M. meandrites</i> in a moderately to well-supported clade with <i>Astrangia</i> sp. (family Astrangidae). This newly assembled mitochondrial genome can be used as a reference to support conservation planning, including biomonitoring of this stony coral using environmental DNA.