DNA Extraction Techniques for Genomic Analyses of Macroalgae

Wilson, Laura J.; Weber, Xénia A.; King, Tania M.; Fraser, Ceridwen I.

doi:10.1007/978-94-017-7534-2_15

Cited by 7 publications

(6 citation statements)

References 42 publications

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“…2) and Chile (Fig. 3) (Wilson et al 2016). Furthermore, the primers we used were developed for M. ectocarpii, and although they also amplify M. braseltonii, there might be other Maullinia or related phytomyxean species affecting these kelp populations that our primers could not detect.…”

Section: Infections Of Maullinia Braseltonii In Chile Andmentioning

confidence: 99%

“…Extractions were diluted 1:100 in MilliQ water to reduce the possibility of alginates blocking PCR processes (see Wilson et al 2016). PCR amplification was conducted in a 20 µl solution, comprising 12.5 µl MilliQ water, 0.2 µl each of forward and reverse 10 mM primers, 4 µl of 1 mM dNTPS, 0.1 µl of PerfectTaq polymerase, 2 µl of PerfectTaq buffer (5Prime) and 1 µl of diluted DN A extraction.…”

Section: Genetic Analysesmentioning

confidence: 99%

See 1 more Smart Citation

Gall-forming protistan parasites infect southern bull kelp across the Southern Ocean, with prevalence increasing to the south

Blake¹,

Thiel²,

López³

et al. 2017

Mar. Ecol. Prog. Ser.

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Section: Infections Of Maullinia Braseltonii In Chile Andmentioning

confidence: 99%

Section: Genetic Analysesmentioning

confidence: 99%

Gall-forming protistan parasites infect southern bull kelp across the Southern Ocean, with prevalence increasing to the south

Blake¹,

Thiel²,

López³

et al. 2017

Mar. Ecol. Prog. Ser.

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“…Although GBS methods generally recommend a large amount of DNA per sample, between 100 and 1000 ng of DNA per sample (Davey et al, 2011;Elshire et al, 2011;Etter et al, 2011), quantities as low as 30 ng can be adequate if the DNA is high quality (e.g. for problematic taxa such as macroalgae that require extensive cleaning to remove inhibitors; Wilson et al, 2016). The availability of a suitable reference genome is worth considering before conducting GBS (Figure 2), as sampling, error rates and filtering requirements are interconnected.…”

Section: Box 1 Biogeography By Any Other Namementioning

confidence: 99%

Genotyping‐by‐sequencing for biogeography

Vaux

Dutoit

Fraser

et al. 2022

Journal of Biogeography

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Aim: Genotyping-by-sequencing (GBS) and similar reduced-representation sequencing methods, such as restriction site-associated DNA sequencing (RADseq), have been revolutionary for genetic analyses in biogeography. However, navigating the many different methodological and analytical approaches and numerous sources of potential error can be overwhelming. We provide an overview of key considerations for biogeographical research using GBS, from sample design through data filtering to the sharing of data, which should particularly assist new users.Taxon: All taxa. Location: Worldwide. Methods:We review recent advances for GBS and compare differences among GBS methods and analytical approaches. We highlight the concerns most relevant for biogeographical research, and emphasise practical limitations for studies on non-model organisms.Results: GBS methods vary substantially and recent literature demonstrates the need for careful study design and data filtering relevant to the study organism and hypothesis under investigation. Biogeographical research using non-model organisms or long-term sampling are likely to face some practical limitations compared to ideal GBS study designs. The methodological information recorded in published manuscripts often varies. We outline a general framework for planning and undertaking biogeographical research using GBS.Main conclusions: GBS and similar approaches have grown rapidly in popularity for biogeographical research. Evaluating, recording and justifying decisions throughout a GBS workflow-across sampling, library preparation and sequencing, identifying and filtering samples and loci, biogeographical analyses, and sharing data-is crucial for improving scientific reproducibility and compatibility among GBS datasets. This review outlines ways to improve and simplify GBS research, thereby enhancing our capacity to use genomic data to address broad-scale biogeographical questions.

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“…Contaminants in algal and plant DNA extractions have long been a source of frustration for molecular biologists (Hoarau et al, 2007; Ramakrishnan et al, 2017; Wilson et al, 2016). As whole genome sequencing (WGS) increasingly replaces more traditional genetic approaches, there is a corresponding need for a shift from extraction methods that yield PCR-grade DNA to WGS-grade DNA extractions (De La Cerda et al, 2023; Jones et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

A Cry For Kelp: Evidence for Polyphenolic Inhibition of Oxford Nanopore Sequencing of Brown Algae

Pearman,

Arranz,

Carvajal

et al. 2024

Preprint

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Genomic resources for macroalgae are increasingly important for conservation and commercial management, however the generation of such resources continues to be hampered by difficulties in the isolation of suitable DNA. Even when DNA has been isolated that otherwise appears high quality, such samples may not perform well during the sequencing process. We here compare Oxford Nanopore long-read sequencing results for three species of macroalgae to those of non-macroalgal species and find that macroalgal samples tend to lead to rapid decline in the number of available sequencing pores resulting in reduced sequencing yield. LC-MS analysis of macroalgal DNA that would be considered suitable for sequencing reveals that DNA derived from dried macroalgae is enriched for polyphenol-DNA adducts – which may lead to sequencing inhibition. Our findings have wide-ranging implications for the generation of genomic resources from macroalgae, for example long read sequencing of dried herbarium specimens, and suggest a need to use fresh tissue wherever possible for genome sequencing.

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DNA Extraction Techniques for Genomic Analyses of Macroalgae

Cited by 7 publications

References 42 publications

Gall-forming protistan parasites infect southern bull kelp across the Southern Ocean, with prevalence increasing to the south

Gall-forming protistan parasites infect southern bull kelp across the Southern Ocean, with prevalence increasing to the south

Genotyping‐by‐sequencing for biogeography

A Cry For Kelp: Evidence for Polyphenolic Inhibition of Oxford Nanopore Sequencing of Brown Algae

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