Development and Optimization of Quantitative PCR Assays to Aid<i>Ostrea lurida</i>Carpenter 1864 Restoration Efforts

Wight, Nathan A.; Suzuki, J.; Vadopalas, Brent; Friedman, Carolyn S.

doi:10.2983/035.028.0108

Cited by 14 publications

(11 citation statements)

References 30 publications

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“…Whereas the Ostrea lurida genome in its entirety has not been sequenced, the CO1 gene region has been successfully amplified, and O. lurida-specific primers and probes for qPCR have been produced (Wight et al 2009). …”

mentioning

confidence: 99%

The Olympia OysterOstrea lurida: Recent Advances in Natural History, Ecology, and Restoration

Pritchard

Shanks

Rimler

et al. 2015

Journal of Shellfish Research

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mentioning

confidence: 99%

The Olympia OysterOstrea lurida: Recent Advances in Natural History, Ecology, and Restoration

Pritchard

Shanks

Rimler

et al. 2015

Journal of Shellfish Research

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“…It has been a challenge to develop a reliable and cost-effective solution for larval identification to handle the large volume of samples required for many field studies. Current successful methods involve multiplex PCR (Hare et al 2000;Larsen et al 2005), quantitative PCR (Wight et al 2009), and fluorescent in situ hybridization with DNA probes (Henzler et al 2010), but each method has specific limitations on sample volume, specificity, and cost per sample.…”

mentioning

confidence: 99%

Semi‐automated image analysis for the identification of bivalve larvae from a Cape Cod estuary

Thompson

Hare

Gallager

2012

Limnology & Ocean Methods

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Machine-learning methods for identifying planktonic organisms are becoming well-established. Although similar morphologies among species make traditional image identification methods difficult for larval bivalves, species-specific shell birefringence patterns under polarized light permit identification by color and texturebased features. This approach uses cross-polarized images of bivalve larvae, extracts Gabor and color angle features from each image, and classifies images using a Support Vector Machine. We adapted this method, which was established on hatchery-reared larvae, to identify bivalve larvae from a series of field samples from a Cape Cod estuary in 2009. This method had 98% identification accuracy for four hatchery-reared species. We used a multiplex polymerase chain reaction (PCR) method to confirm field identifications and to compare accuracies to the software classifications. Image classification of larvae collected in the field had lower accuracies than both the classification of hatchery species and PCR-based identification due to error in visually classifying unknown larvae and variability in larval images from the field. A six-species field training set had the best correspondence to our visual classifications with 75% overall agreement and individual species agreements from 63% to 88%. Larval abundance estimates for a time-series of field samples showed good correspondence with visual methods after correction. Overall, this approach represents a cost-and time-saving alternative to molecular-based identifications and can produce sufficient results to address long-term abundance and transport-based questions on a species-specific level, a rarity in studies of bivalve larvae.

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“…The molecular revolution has produced new techniques that allow rapid diagnosis of pathogens (e.g., Reece et al, 1997Reece et al, , 2008De Faveri et al, 2009;Wight et al, 2009;Wilbur et al, 2012). Whereas in the past, epidemiologists to a large extent relied on often ineffective culturing techniques and histology to identify marine pathogens, species-specific DNA probes now enable screening for a broad range of pathogens (e.g., Harvell et al, 1999).…”

Section: Emerging Diseases Stressors and Associated Ecological Impactsmentioning

confidence: 99%

The ecology, evolution, impacts and management of host–parasite interactions of marine molluscs

Coen

Bishop

2015

Journal of Invertebrate Pathology

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Development and Optimization of Quantitative PCR Assays to AidOstrea luridaCarpenter 1864 Restoration Efforts

Cited by 14 publications

References 30 publications

The Olympia OysterOstrea lurida: Recent Advances in Natural History, Ecology, and Restoration

The Olympia OysterOstrea lurida: Recent Advances in Natural History, Ecology, and Restoration

Semi‐automated image analysis for the identification of bivalve larvae from a Cape Cod estuary

The ecology, evolution, impacts and management of host–parasite interactions of marine molluscs

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