A Cost-effective DNA Isolation Strategy from Crustaceans Enables the First Molecular Phylogenetic Identification of Moina macrocopa from India

Abstract

We report the first barcode identification of water flea species Moina macrocopa (strain JSK1) from the Indian subcontinent. The strain isolated from a freshwater pond near Mumbai by collective efforts of CUBE (Collaborative Undergraduate Biology Education), was morphologically characterized as Moina species. Keeping up with the growing demand of affordable science in colleges and to avoid hazardous technologies, we established a home grown porcelain-abrasion DNA extraction strategy for crustaceans, and compared it against routinely used protocols employing liquid nitrogen or insect-DNA isolation kits. Our method successfully yielded high quality genomic DNA from Moina, comparable to published protocols as further analysed by restriction digestion, ligation and PCR efficiency. We also sequenced two barcoding loci namely, COI and ITS sequences, duly submitted and curated by Genbank (accession numbers MH734122.1 and MH745035.1). Molecular phylogenetic analyses identified the Indian species as Moina macrocopa and related it closely to the Russian clade. Protein prediction analyses of the variations in COI revealed that the missense mutations lie in the aliphatic membrane helices and should not affect the catalytic capacity of cytochrome oxidase. The strain JSK1 is currently disseminated and maintained collectively by CUBE students across India, towards developing it as a model system.