Abstract
Non-lethal DNA sampling has long appealed to researchers studying population and conservation genetics, as it does not necessitate removing individuals permanently from their natural environment or destroying valuable samples. However, such an approach has not yet been well established in bivalves. In this study, we demonstrate that the gill represents a good source of tissue for non-lethal sampling in scallops. Removal of a few gill filaments caused no noticeable behavioral abnormalities or increased mortality rates in Zhikong scallop (Chlamys farreri) during a three-month period of observation. To facilitate rapid gill-based DNA extraction, six methods (MA-MF) were designed and evaluated, each requiring less than one hour of processing time. The optimal method was identified as MF, in terms of maintaining DNA integrity and genotyping accuracy. Further optimization of MF method by orthogonal experimental design suggested that the utilization of gills could be limited to 2 mg of sample, which is sufficient for performing up to 20,000 PCR reactions. We also demonstrate the excellent cross-species utility of MF in two additional scallop species, Yesso scallop (Patinopecten yessoensis) and bay scallop (Argopecten irradians). Taken together, our study provides a rapid and efficient approach for applying non-lethal DNA sampling in bivalve species, which would serve as a valuable tool for maintaining bivalve populations and conservation genetics, as well as in breeding studies.
Highlights
Scallops are a diverse group of animals consisting of more than 300 extant species that are distributed in ocean regions worldwide
Comparison of DNA Yield between Gill and Mantle We further evaluated whether the gill could serve as a good substitute for the mantle with respect to DNA yield
Genomic DNA was extracted from the same amount of gills and mantles from three Zhikong scallops using a different amount of starting material
Summary
Scallops are a diverse group of animals consisting of more than 300 extant species that are distributed in ocean regions worldwide It is well-established that they play a prominent role in the structure and function of local benthic ecosystems [1]. The isolation of high-quality DNA is traditionally not a trivial task in molluscs due to the secretion of mucopolysaccharide and polyphenolic proteins that could copurify with DNA and interfere with the enzymatic processing of nucleic acids [2] To address this issue, several specialized DNA extraction protocols [2,3,4], as well as commercial kits (e.g., E.Z.N.A.H Mollusc DNA kit from Omega Bio-Tek), have been developed that present modifications from those developed in mammals or plants. These methods are generally laborious and time-consuming, and sometimes require a relatively large amount of sample materials that would have to sacrifice the animals under study to ensure sufficient amount of DNA for downstream applications
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