Abstract
Daphnia galeata is an important plankton in aquatic ecosystems. As a widely distributed species, D. galeata has been found throughout the Holarctic region. Understanding the genetic diversity and evolution of D. galeata requires the accumulation of genetic information from different locations. Even though the mitochondrial genome (mitogenome) sequence of D. galeata has already been reported, little is known about the evolution of its mitochondrial control region. In this study, D. galeata samples were collected from the Han River on the Korean Peninsula and its partial nd2 gene was sequenced for haplotype network analysis. This analysis showed that four clades of D. galeata were present in the Holarctic region. Moreover, the D. galeata examined in this study belonged to clade D and was specific to South Korea. The mitogenome of D. galeata from the Han River showed similar gene content and structure compared to sequences reported from Japan. Furthermore, the structure of control region of the Han River was similar to those of Japanese clones and differed substantially from European clone. Finally, a phylogenetic analysis based on the amino acid sequences of 13 protein-coding genes (PCGs) indicated that D. galeata from the Han River formed a cluster with clones collected from Lakes Kasumigaura, Shirakaba, and Kizaki in Japan. The differences in control region structure and stem and loop structure reflect the different evolutionary directions of the mitogenomes from Asian and European clones. These findings improve our understanding of the mitogenome structure and genetic diversity of D. galeata.
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Data availability
The data that support the findings of this study are openly available in Genbank under the accession number OM397534.
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Acknowledgements
We acknowledged Jong-Won Baek and Min-Ho Mun (Sangmyung University, South Korea) sample collection for the assistance of sample collection in field.
Funding
This work was supported by the National Research Foundation of South Korea (NRF) grant funded by the South Korea government (MSIP) (No. NRF-2016M3A9E1915578).
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All authors contributed to the study conception and design. Material preparation, data collection, and analysis were performed by CBK, TJC, TDD, and JIK. The first draft of the manuscript was written by TJC and TDD and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.
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ESM 1:
Table S1 nd2 sequences of Daphnia galeata obtained for haplotype network analysis from Genbank used in this study. Table S2 Similarity of orthologous alpha/alpha’ and gamma/gamma’ of Daphnia galeata.Fig. S1 Median-Joining network of haplotypes based on the variation of the mitochondrial nd2 gene observed in the Holarctic populations of Daphnia galeata, Blue indicates the Han River clone analyzed in this study. Mutated positions are shown as branch lines.Fig. S2 Transfer RNA secondary structures for Daphnia galeata collected from the Han River, South Korea.Fig. S3 Phylogenetic relationships of Daphnia galeata based on amino acid sequences of 13 PCGs. Black circle indicates the newly sequenced mitogenome in this study. GenBank accession numbers are indicated next to species names. Possibility values (left) and bootstrap values (right) are shown at the nodes. (DOCX 327 kb)
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Choi, TJ., Do, T.D., Kim, JI. et al. Analysis of the complete mitogenome of Daphnia galeata from the Han River, South Korea: structure comparison and control region evolution. Funct Integr Genomics 23, 65 (2023). https://doi.org/10.1007/s10142-023-00986-5
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DOI: https://doi.org/10.1007/s10142-023-00986-5