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Open AccessArticle
The Mitogenomic Landscape of Hexacorallia Corals: Insight into Their Slow Evolution
by
Zhanfei Wei
Zhanfei Wei 1,2,†,
Yang Yang
Yang Yang 2,3,†,
Lihui Meng
Lihui Meng 4,
Nannan Zhang
Nannan Zhang 2,
Shanshan Liu
Shanshan Liu 2,
Liang Meng
Liang Meng 2,*,
Yang Li
Yang Li 5
and
Changwei Shao
Changwei Shao 1,*
1
State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
2
BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
3
College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
4
School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
5
Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2024, 25(15), 8218; https://doi.org/10.3390/ijms25158218 (registering DOI)
Submission received: 8 April 2024
/
Revised: 10 July 2024
/
Accepted: 17 July 2024
/
Published: 27 July 2024
Abstract
The utility of the mitochondrial genomes (mitogenomes) in analyzing the evolutionary history of animals has been proven. Five deep-sea corals (Bathypathes sp.1, Bathypathes sp.2, Schizopathidae 1, Trissopathes sp., and Leiopathes sp.) were collected in the South China Sea (SCS). Initially, the structures and collinearity of the five deep-sea coral mitogenomes were analyzed. The gene arrangements in the five deep-sea coral mitogenomes were similar to those in the order Antipatharia, which evidenced their conservation throughout evolutionary history. Additionally, to elucidate the slow evolutionary rates in Hexacorallia mitogenomes, we conducted comprehensive analyses, including examining phylogenetic relationships, performing average nucleotide identity (ANI) analysis, and assessing GC-skew dissimilarity combining five deep-sea coral mitogenomes and 522 reference Hexacorallia mitogenomes. Phylogenetic analysis using 13 conserved proteins revealed that species clustered together at the order level, and they exhibited interspersed distributions at the family level. The ANI results revealed that species had significant similarities (identity > 85%) within the same order, while species from different orders showed notable differences (identity < 80%). The investigation of the Hexacorallia mitogenomes also highlighted that the GC-skew dissimilarity was highly significant at the order level, but not as pronounced at the family level. These results might be attributed to the slow evolution rate of Hexacorallia mitogenomes and provide evidence of mitogenomic diversity. Furthermore, divergence time analysis revealed older divergence times assessed via mitogenomes compared with nuclear data, shedding light on significant evolutionary events shaping distinct orders within Hexacorallia corals. Those findings provide new insights into understanding the slow evolutionary rates of deep-sea corals in all lineages of Hexacorallia using their mitogenomes.
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MDPI and ACS Style
Wei, Z.; Yang, Y.; Meng, L.; Zhang, N.; Liu, S.; Meng, L.; Li, Y.; Shao, C.
The Mitogenomic Landscape of Hexacorallia Corals: Insight into Their Slow Evolution. Int. J. Mol. Sci. 2024, 25, 8218.
https://doi.org/10.3390/ijms25158218
AMA Style
Wei Z, Yang Y, Meng L, Zhang N, Liu S, Meng L, Li Y, Shao C.
The Mitogenomic Landscape of Hexacorallia Corals: Insight into Their Slow Evolution. International Journal of Molecular Sciences. 2024; 25(15):8218.
https://doi.org/10.3390/ijms25158218
Chicago/Turabian Style
Wei, Zhanfei, Yang Yang, Lihui Meng, Nannan Zhang, Shanshan Liu, Liang Meng, Yang Li, and Changwei Shao.
2024. "The Mitogenomic Landscape of Hexacorallia Corals: Insight into Their Slow Evolution" International Journal of Molecular Sciences 25, no. 15: 8218.
https://doi.org/10.3390/ijms25158218
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