Journal Article

Complete mitogenomes reveal high diversity and recent population dynamics in Antarctic krill

Seim, Inge, Wei, Zhanfei, Li, Shuo, Shao, Changwei, Yang, Xianwei, Liu, Kaiqiang, Fan, Guangyi, Liu, Xin, Du, Xiao, Sun, Shuai

2025

Overview

Background The Antarctic krill ( Euphausia superba ) is a keystone species in the Southern Ocean ecosystem, influencing food web dynamics and ecosystem functionality. Despite its ecological importance, further exploration is essential to understand their population dynamics. Results In this study, we present the complete mitogenome of the Antarctic krill. The assembly is 18,926 bp, including a notably large 3,952 bp control region (CR). The CR features a satellite repeat spanning 2,289 bp, showcasing the effectiveness of long-read sequencing in resolving complex genomic regions. Additionally, we identified 900 nuclear-mitochondrial segments (NUMTs) totaling 2.79 Mb, shedding light on the dynamic integration of mitochondrial DNA (mtDNA) into the nuclear genomes. By establishing a dataset comprising 80 krill mitogenomes, we unveil substantial mitochondrial diversity, particularly within the ND4 gene. While our analysis reveals no significant differentiation among four geographically distinct groups, we identify at least four maternal genetic clusters. Haplotype network analysis and demographic reconstructions suggest a recent population expansion, likely driven by favorable environmental conditions during the late Pleistocene. Furthermore, our investigation into selection pressures on mitochondrial genes reveals evidence of purifying selection across all 13 protein-coding genes, underscoring the pivotal role of mtDNA conservation in maintaining mitochondrial function under extreme environments. Conclusions This study provides a repository of Antarctic krill mitogenomes and insights into the population genetics and evolutionary history of this ecologically important species from a mitogenomic perspective, with implications for krill conservation and management in the Southern Ocean.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Animal genetics / Animal Genetics and Genomics / Animal populations / Animals / Antarctic krill / Antarctic Regions / Biological diversity / Biomedical and Life Sciences / Cluster analysis / Conservation / Datasets / DNA, Mitochondrial - genetics / Ecological function / Environmental conditions / Euphausiacea / Euphausiacea - classification / Euphausiacea - genetics / Evolution & development / Evolutionary genetics / Extreme environments / Food chains / Food webs / Genes / Genetic analysis / Genetic aspects / Genetic diversity / Genetic research / Genetic Variation / Genetics / Genome, Mitochondrial / Genomes / Genomics / Haplotypes / Keystone species / Krill / Life Sciences / Marine ecosystems / Microarrays / Microbial Genetics and Genomics / Mitochondrial DNA / Mitochondrial genome / Natural selection / ND4 gene / Network analysis / Phylogeny / Physiological aspects / Plant Genetics and Genomics / Pleistocene / Population Dynamics / Population genetics / Population growth / Proteomics / Transfer RNA