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 aims to assess the efficiency of DNA extraction and its quality in Gammarus (Gammarus spp.) from various water bodies of Kazakhstan, as well as to test the reproducibility of COI gene amplification using PCR for subsequent genetic identification of the samples.

Materials and Methods. In the course of the study, Gammarus samples (Gammarus spp.) were collected from various freshwater bodies in northern, southern, and eastern Kazakhstan.

The study aimed to assess the quality and quantity of extracted DNA, as well as the reproducibility of the mitochondrial gene fragment amplification. The extraction protocol was adapted to account for the specific characteristics of amphipod tissues.

Results. The obtained 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 concentration of nucleic acids varied from 191.6 to 232.0 ng/μL, which meets the requirements for subsequent PCR amplification. The results confirm the applicability of the developed approach for subsequent molecular-genetic analysis and identification of Gammarus in the water bodies of Kazakhstan.

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