Phylogenetics and Mitogenome Organisation in Black Corals (Anthozoa: Hexacorallia: Antipatharia): An Order-Wide Survey Inferred From Complete Mitochondrial Genomes

Abstract

Black corals (Anthozoa: Antipatharia) are an ecologically and culturally important group of deep-sea cnidarians. However, as the majority of species inhabit depths >50 m, they are relatively understudied. The inaccessibility of well-preserved tissue for species of interest has limited the scope of molecular analysis, and as a result only a small number of antipatharian mitochondrial genomes have been published. Using next generation sequencing, 18 complete and five partial antipatharian mitochondrial genomes were assembled, increasing the number of complete mitochondrial genomes to 22. This includes species from six antipatharian families, four of which were previously unrepresented, enabling the first family-level, full mitochondrial gene analysis over the whole order. The circular mitogenomes ranged in size from 17,681 to 21,669 bp with the large range in size due to the addition of an intron in COX1 in some species and size variation of intergenic regions. All mitogenomes contained the genes standard to all hexacoral mitogenomes (13 protein coding genes, two rRNAs and two tRNAs). The only difference in gene content is the presence of the COX1 intron in five families. The most variable mitochondrial gene is ND4 which may have implications for future barcoding studies. Phylogenetic analysis confirms that Leiopathidae is sister to all other families. Families Antipathidae, Cladopathidae and Schizopathidae are polyphyletic, supporting previous studies that call for a taxonomic revision.

Widest geographic distribution of a shallow and mesophotic antipatharian coral (Anthozoa: Hexacorallia): Antipathes grandis VERRILL, 1928 – confirmed by morphometric and molecular analyses

“…Confirmation of its taxonomic identity will necessitate examination of other individuals. For instance, sequencing additional mtDNA markers that have recently been proposed to be more variable (nad4; Barrett et al 2020), and application of next generation sequencing techniques (e.g., ultraconserved elements and exon loci; Quattrini et al 2018). The red morphotype from Madagascar was genetically identical to the Hawaiian A. grandis across 817 bp of IGR-cox1, which validates its identification as A. grandis.…”

Complete mitochondrial genomes of two species of Stichopathes Brook, 1889 (Hexacorallia: Antipatharia: Antipathidae) from Rapa Nui (Easter Island)

“…Both mitogenomes presented the classic pattern expected for Hexacorallia of 13 protein-coding genes, two rRNA genes, and two tRNA genes (tRNA -met and tRNA -trp ) plus a COX1 intron with embedded HEG as found in Antipathidae and other antipatharian families (Barrett et al 2020 ). The complete mitogenome of Stichopathes sp.…”

“…Antipathidae is composed of eight genera distinguished by morphological differences in colony branching pattern, polyps, and skeletal spines (Molodtsova and Opresko 2021 ). Recent phylogenetic studies based on the internal transcriber spacer 1 and 2 ( ITS1 and ITS2 ) rDNA (Bo et al 2012 ) and mitochondrial genomes (Barrett et al 2020 ) indicate that Antipathidae and several genera within Antipathidae are not monophyletic, highlighting the need for future taxonomic revisions.…”

“…These findings highlight the need for further phylogenetic studies and taxonomic revisions within Antipathidae. With only a few complete antipatharian mitogenomes available, the distinction of clades even at the family level is hindered (Barrett et al 2020 ). Yet, phylogenetic information based on mitochondrial genomes is critical to understand evolutionary history and phylogeography and to provide insight into which taxa to prioritize for taxonomic revisions.…”

Mitogenomes Reveal Alternative Initiation Codons and Lineage-Specific Gene Order Conservation in Echinoderms

“…Mitogenome sequences are frequently used in downstream applications such as population genomics and phylogenomics ( Quek et al. 2019 ; Barrett et al. 2020 ; Inoue et al.…”