Assessment of DNA extraction efficiency and quality in Gammarus spp. (Crustacea: Amphipoda) from various water bodies of Kazakhstan

Abstract

Background and Aim. Amphipods of the genus Gammarus are widely distributed in freshwater ecosystems of the Northern Hemisphere and are commonly used as model organisms in ecological, toxicological, and molecular studies. However, morphological identification of Gammarus is complicated due to the high degree of intraspecific variability and the presence of cryptic species. This makes molecular approaches based on mitochondrial DNA analysis (e.g., the COI gene) particularly important for taxonomic verification and biodiversity assessment. This study aimed to assess the efficiency of DNA extraction and its quality in Gammarus (Gammarus spp.) from various water bodies in Kazakhstan, and to test the reproducibility of COI gene amplification using PCR for subsequent genetic identification.

Materials and Methods. Gammarus spp. samples (Gammarus spp.) were collected from various freshwater bodies in northern, southern, and eastern Kazakhstan. The DNA extraction protocol was adapted to account for the specific characteristics of amphipod tissues.

Results. The extracted DNA samples demonstrated satisfactory purity and concentration, ensuring successful PCR amplification. All samples showed satisfactory DNA purity, with A260/A280 ratios ranging from 1.69 to 2.00, indicating the absence of significant protein contamination. The nucleic acid concentration varied from 191.6 to 232.0 ng/μL, which meets the requirements for subsequent PCR amplification. The results confirm the applicability of the optimized approach for molecular-genetic analysis and identification of Gammarus in the water bodies of Kazakhstan.

Conclusion. This study successfully optimized a DNA extraction protocol for Gammarus samples collected from freshwater bodies in Kazakhstan, yielding DNA of satisfactory purity and concentration suitable for PCR amplification. The successful visualization of the amplified COI gene fragment on an agarose gel provides a foundation for further population-genetic studies of amphipods in the region.