Creating and Comparing DNA Tools for Identifying Marine Shellfish

Jenn Hoskins
1st June, 2024

Creating and Comparing DNA Tools for Identifying Marine Shellfish

In silico analysis of new and previously published primers reveals considerable variation in amplification performance, with many primers showing either low specificity by amplifying non-molluscan DNA or low universality by targeting only specific mollusk groups.

Image adapted from: Shi et al. / CC BY (Source)

Key Findings

  • Researchers from Shanghai Jiao Tong University developed new primers for eDNA analysis to monitor marine mollusk biodiversity
  • The primer MollCOI253 showed superior performance in amplifying DNA from a wide range of mollusk species
  • This study enhances the ability to monitor and conserve marine biodiversity using non-invasive eDNA technology
Marine mollusks are a diverse group of organisms that play crucial roles in marine ecosystems, yet monitoring their biodiversity remains a significant challenge due to their extensive diversity and widespread distribution. Traditional methods for surveying marine life often involve invasive techniques that can be selective and limited in scope[2]. Environmental DNA (eDNA) technology has emerged as a promising tool for biodiversity monitoring, offering a non-invasive and comprehensive approach. However, relevant studies on marine mollusks have been limited. A recent study conducted by researchers from Shanghai Jiao Tong University aimed to address this gap by developing and validating new primers for eDNA analysis of marine mollusks[1]. Primers are short sequences of nucleotides that provide a starting point for DNA synthesis, essential for amplifying specific DNA regions in eDNA samples. The study designed seven new primers for the mollusk community and compared them with eight previously published primers to identify the most effective ones. The researchers first conducted in silico tests, which are computer simulations used to predict the behavior of the primers. Two of the new primers, MollCOI154 and MollCOI255, showed non-specific amplification, meaning they could potentially amplify DNA from non-target organisms. This issue was also observed in some of the published primers (COI204, Sepi, and veneroida). Additionally, three of the new primers (Moll12S100, Moll12S195, and Moll16S) failed to amplify DNA across all tested mollusk samples. The study then proceeded to test the remaining primers on four eDNA samples collected from the Yangtze River estuary. Except for Moll16S, all the developed primers and two published primers (unionoida and veneroida) successfully amplified DNA from these samples. Among them, the primer MollCOI253 demonstrated superior performance in terms of amplification success and specificity. It provided higher annotation of the amplification results compared to the other primers, indicating its effectiveness in detecting a wide range of mollusk species. This study builds on previous research that has demonstrated the potential of eDNA for monitoring aquatic biodiversity. For instance, eDNA has been successfully used to survey fish populations in marine environments[2] and freshwater mussels[3], highlighting its versatility and effectiveness. The current study's findings align with these earlier results, further validating eDNA as a valuable tool for biodiversity monitoring. Moreover, the development of ecoPrimers, a software for identifying new barcode markers, has facilitated the discovery of efficient primers for various taxa[4]. The success of MollCOI253 in this study underscores the importance of using advanced bioinformatics tools to optimize eDNA analysis. The research conducted by Shanghai Jiao Tong University not only provides a new set of tools for monitoring marine mollusk biodiversity but also contributes to the broader field of eDNA research. By identifying an effective primer (MollCOI253), this study enhances our ability to assess and conserve marine biodiversity. The use of eDNA technology, supported by well-designed primers, offers a non-invasive, comprehensive, and efficient method for monitoring marine ecosystems, addressing the limitations of traditional survey techniques. In summary, the study demonstrates that eDNA technology, when equipped with optimized primers like MollCOI253, can significantly improve our ability to monitor and conserve marine mollusk biodiversity. This advancement holds great promise for future research and conservation efforts, ensuring that we can better understand and protect the rich diversity of life in our oceans.

EnvironmentGeneticsMarine Biology

References

Main Study

1) Development of environmental DNA metabarcoding primers for marine mollusks and comparison with published primers

Published 31st May, 2024

https://doi.org/10.1186/s12862-024-02265-8

Related Studies

2) Detection of a diverse marine fish fauna using environmental DNA from seawater samples.

https://doi.org/10.1371/journal.pone.0041732

3) Environmental DNA (eDNA) Shedding and Decay Rates to Model Freshwater Mussel eDNA Transport in a River.

https://doi.org/10.1021/acs.est.7b05199

4) ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis.

https://doi.org/10.1093/nar/gkr732


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