Abstract
The order Dendrochirotida (Class Holothuroidea) is a species-rich echinoderm group, yet its internal evolutionary history remains poorly resolved due to limited mitogenomic resources. In this study, we characterized the first complete mitochondrial genome of Ocnus glacialis and conducted comparative analyses to elucidate its phylogenetic position and molecular evolutionary patterns. The circular mitogenome of O. glacialis is 16,776 bp in length, containing the canonical set of 37 genes. Among the analyzed dendrochirotids, O. glacialis exhibited the highest A + T content (70.88%) and a near-zero AT-skew, a compositional profile often linked to lineage-specific evolution in specialized environments. Selection pressure analyses, including branch-model tests, revealed that these compositional features are associated with relaxed purifying selection and an accelerated rate of sequence evolution. Branch-site analyses further identified specific codon sites in cytb, nad2, nad4l, nad5, and nad6 under positive or relaxed constraints. Structurally, O. glacialis displayed the most complex gene rearrangement pattern among the studied species, characterized by multiple tandem duplication-random loss (TDRL) events and extensive intergenic sequences. Furthermore, divergence time estimation suggests that these structural and compositional shifts occurred in tandem with the lineage’s diversification. We propose that these mitogenomic signatures reflect a synergistic outcome of habitat transition toward Arctic cold-water and deep-sea environments, coupled with demographic factors such as reduced effective population sizes inherent to its benthic life history. By resolving taxonomic uncertainties, this study provides a robust temporal and molecular framework for understanding the evolutionary history and ecological diversification of the Ocnus lineage.
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Acknowledgements
The sample was provided by Drs. Ji-Hoon Kihm and Tae-Yoon Park (Korea Polar Research Institute).
Funding
This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education (RS-2025-00563999). This work was also supported by the Korea Environment Industry & Technology Institute (KEITI) through the Aquatic Ecosystem Conservation Research Program, funded by the Korea Ministry of Environment (MOE) (RS-2022-KE002117).
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Do, S.D., Lee, Y. & Rhee, JS. Comparative mitogenomics of Ocnus glacialis reveals lineage-specific evolutionary rates and complex gene rearrangements in Dendrochirotida.
Sci Rep (2026). https://doi.org/10.1038/s41598-026-59110-9
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DOI: https://doi.org/10.1038/s41598-026-59110-9
Keywords
- Complete mitogenome
- Sea cucumber
- Phylogenetic analysis
- Tandem duplication followed by random loss
- Deep-sea
- Arctic
Source: Ecology - nature.com
