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Cheryl L. Ames

Field-forward sequencing with Oxford Nanopore technology: a strategy to establish the upside-down mangrove jellyfish Cassiopea xamachana as a bioindicator

About Cheryl L. Ames

Cheryl L. Ames is a National Academies of Sciences (NRC) Postdoctoral Fellow at the United States Naval Research Laboratory and a Research Associate at the National Museum of Natural History, Smithsonian Institution in Washington, DC. As an expert in jellyfish and their evolutionary novelties, such as their venom, vision and sex, Cheryl uses a MinION-based field-forward environmental DNA sequencing protocol to assess biodiversity in marine ecosystems, such as coastal mangroves, the Gulf Stream and public aquaria. Cheryl has a Ph.D. in Biological Sciences from the University of Maryland, USA, a Master’s degree in Marine Biology from the University of the Ryukyus in Okinawa, Japan and undergraduate degrees from Queen’s University and the University of Ottawa in Canada. 

Abstract

The combined relative ease of operation, high throughput and reduced cost of NGS platforms has enabled the coupling of traditional field collection methods with laboratory-based metagenomic approaches to provide a molecular snapshot of species-diversity in a plethora of aquatic environments. However, the often-extensive time-lag between field sampling, sequencing and endpoint bioinformatics analyses precludes the ability to provide a contemporaneous characterization of the target ecosystem, against the backdrop of briskly shifting global climate. Furthermore, the growing decline of healthy aquatic ecosystems due to chemical, physical and biological threats, along with concerns related to invasive species and natural disasters, highlights the critical need for field-forward sequencing protocols to provide rapid characterization of a diversity of environmental systems. The recent publication of the reference genome of the upside-down mangrove jellyfish, Cassiopea xamachana, has gained this emerging model species attention as an indicator species with promising applications for coastal ecosystem management and conservation. Taking advantage of the versatility offered by Oxford Nanopore sequencing, we developed a field-forward DNA environmental metabarcoding strategy to characterize Florida Keys mangrove ecosystems, inhabited by C. xamachana, in the year following the catastrophic landfall of Hurricane Irma in 2017. The prototype for this portable system boasts a low-complexity protocol requiring minimal training for operation, a relatively short sample-to-answer timeframe i.e. several hours, field-forward DNA metabarcoding capabilities in austere environments, manual and/or battery-powered equipment with ease of portability and minimal footprint, as well as multiplexing capabilities for the simultaneous assessment of multiple collection sites and/or genetic markers. We present here the first ever eDNA assessment of C. xamachana populations in several Florida Key coastal environments in the wake of a devastating natural disaster, based on the findings of our inaugural field-forward sequencing study.

Cheryl Ames

Cheryl Ames

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