Characterization of the complete mitochondrial genome sequences of three Merulinidae corals and novel insights into the phylogenetics

Abstract

Over the past few decades, modern coral taxonomy, combining morphology and molecular sequence data, has resolved many long-standing questions about scleractinian corals. In this study, we sequenced the complete mitochondrial genomes of three Merulinidae corals (Dipsastraea rotumana, Favites pentagona, and Hydnophora exesa) for the first time using next-generation sequencing. The obtained mitogenome sequences ranged from 16,466 bp (D. rotumana) to 18,006 bp (F. pentagona) in length, and included 13 unique protein-coding genes (PCGs), two transfer RNA genes, and two ribosomal RNA genes . Gene arrangement, nucleotide composition, and nucleotide bias of the three Merulinidae corals were canonically identical to each other and consistent with other scleractinian corals. We performed a Bayesian phylogenetic reconstruction based on 13 protein-coding sequences of 86 Scleractinia species. The results showed that the family Merulinidae was conventionally nested within the robust branch, with H. exesa clustered closely with F. pentagona and D. rotumana clustered closely with Favites abdita. This study provides novel insight into the phylogenetics of species within the family Merulinidae and the evolutionary relationships among different Scleractinia genera.

Molecular phylogenetic relationships based on mitochondrial genomes of novel deep-sea corals (Octocorallia: Alcyonacea): Insights into slow evolution and adaptation to extreme deep-sea environments

“…The purifying selection of cold-water corals indicated that the deep-sea environment variation might be insufficient to induce alterations in genetic functionality. In addition, the atp8 gene, which plays an important role in ATP synthesis, exhibited the highest median K a/ K s value in selected cold-water coral species, consistent with previous studies in other organisms ( Kumar et al, 2020 ; Lv et al, 2018 ; Niu et al, 2020 ). Based on their higher K a/ K s ratios and increased amino acid changes, the atp8 and mutS genes may have evolved more rapidly, experiencing more relaxed selective constraints and accumulating more mutations.…”

The Complete Mitochondrial Genome of Homophyllia bowerbanki (Scleractinia, Lobophylliidae): The First Sequence for the Genus Homophyllia

“…Identifying the driving force that shaped the GC content and deciphering the biological meaning of variations in the GC content will help us understand genome evolution [ 25 ]. The mitogenome GC content of most scleractinians ranged from 30% to 40% [ 22 , 26 , 27 , 28 ]. The intergenic regions of different genes ranged from −1 to 1506 bp.…”

Characterization of the complete mitochondrial genome of Diploastrea heliopora and phylogeny of the scleractinia species which have group I introns in their COI genes

“…PCR reaction mixture was totally 25 μL, including template DNA 1 μL, primers (forward and reverse) 2 μL, dNTPs 2 μL, Taq DNA polymerase 0.15 μL, buffer solution 2.5 μL, and sterile deionized water. The Eppendorf thermal cycler was used for PCR amplification following the standard procedures performed in Niu et al (2020) . The amplified products were purified and bidirectional sequenced in Personal Biotech.…”

“…The mitochondrial genomes of Anthozoa are atypical with a few distinguishing characteristics. It is manifested in the presence of conventional two tRNAs; All protein-coding genes (PCGs) stop the protein biosynthesis process with complete termination codons ( Fukami and Knowlton, 2005 , Niu et al, 2020 ); A DNA mismatch repair mechanism benefiting from the slow mutation rates ( Shearer et al, 2002 ); The relatively loose gene packing, featured by a series of noncoding regions ( Kitahara et al, 2014 ); And group I introns interrupting functional genes ( Beagley et al, 1998 , Emblem et al, 2011 ).…”