Mitogenomic Characterization and Phylogenetic Placement of African Hind, Cephalopholis taeniops: Shedding Light on the Evolution of Groupers (Serranidae: Epinephelinae)

Author:

Kundu Shantanu1ORCID,Kang Hye-Eun2ORCID,Kim Ah Ran3ORCID,Lee Soo Rin3ORCID,Kim Eun-Bi4ORCID,Amin Muhammad Hilman Fu’adil5ORCID,Andriyono Sapto6ORCID,Kim Hyun-Woo37ORCID,Kang Kyoungmi8ORCID

Affiliation:

1. Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea

2. Institute of Marine Life Science, Pukyong National University, Busan 48513, Republic of Korea

3. Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea

4. Ocean Georesources Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea

5. Advance Tropical Biodiversity, Genomics, and Conservation Research Group, Department of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia

6. Department of Marine, Faculty of Fisheries and Marine, Airlangga University, Surabaya 60115, Indonesia

7. Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea

8. International Graduate Program of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea

Abstract

The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure of and variations in Cephalopholis species mitogenomes, along with their phylogenetic relationships, focusing specifically on Cephalopholis taeniops from the Eastern Atlantic Ocean. The generated mitogenome spans 16,572 base pairs and exhibits a gene order analogous to that of the ancestral teleost’s, featuring 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. The mitogenome of C. taeniops displays an AT bias (54.99%), aligning with related species. The majority of PCGs in the mitogenome initiate with the start codon ATG, with the exceptions being COI (GTG) and atp6 (TTG). The relative synonymous codon usage analysis revealed the maximum abundance of leucine, proline, serine, and threonine. The nonsynonymous/synonymous ratios were <1, which indicates a strong negative selection among all PCGs of the Cephalopholis species. In C. taeniops, the prevalent transfer RNAs display conventional cloverleaf secondary structures, except for tRNA-serine (GCT), which lacks a dihydrouracil (DHU) stem. A comparative examination of conserved domains and sequence blocks across various Cephalopholis species indicates noteworthy variations in length and nucleotide diversity. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic analyses, employing the concatenated PCGs and a combination of PCGs + rRNAs, distinctly separate all Cephalopholis species, including C. taeniops. Overall, these findings deepen our understanding of evolutionary relationships among serranid groupers, emphasizing the significance of structural considerations in mitogenomic analyses.

Funder

National Research Foundation of Korea

Publisher

MDPI AG

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