Analyses of ITS and LSU gene regions provide congruent results on fungal community responses

Brown, Shawn P.; Rigdon-Huss, Anne R.; Jumpponen, Ari

doi:10.1016/j.funeco.2014.02.002

Cited by 45 publications

(35 citation statements)

References 15 publications

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“…There are species-specific biases in DNA extraction and amplification. When choosing a primer pair, trade-offs between quality stringency and quantification are inevitable (Amend et al 2010;Waud et al 2014), and targetting different sequences may skew the results, though at least one study showed congruent results with ITS or LSU sequences (Brown et al 2014).…”

Section: Who Is There?mentioning

confidence: 99%

Aquatic hyphomycetes in a changing environment

Bärlocher

2016

Fungal Ecology

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Section: Who Is There?mentioning

confidence: 99%

Aquatic hyphomycetes in a changing environment

Bärlocher

2016

Fungal Ecology

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“…After this quality control, ~ 50% of the OTUs were singletons, which we extracted into four fasta files (supplemental material) containing all comparable singleton sequences (ITS1-FLX, ITS1-Titanium, ITS2 and LSU). LSU libraries were aligned against a modified James et al (2006) reference (Brown et al 2014) and gaps removed prior to downstream analyses. Sequences were truncated to equal lengths and subsampled to equal numbers per library (Table S1).…”

mentioning

confidence: 99%

Scraping the bottom of the barrel: are rare high throughput sequences artifacts?

et al. 2015

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“…; Brown et al . ). These effects might also depend on the taxonomic scale at which the data are examined.…”

Section: Discussionmentioning

confidence: 97%

“…) where nonfungal sequences were removed and remaining sequences were de novo aligned using MUSCLE ( see Brown et al . ). We identified and culled potential chimeras using UCHIME (Edgar et al .…”

Section: Methodsmentioning

confidence: 97%

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Don't put all your eggs in one basket: a cost‐effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array

Brown

Ferrer

Dalling

et al. 2016

Molecular Ecology Resources

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With the increasing democratization of high-throughput sequencing (HTS) technologies, along with the concomitant increase in sequence yield per dollar, many researchers are exploring HTS for microbial community ecology. Many elements of experimental design can drastically affect the final observed community structure, notably the choice of primers for amplification prior to sequencing. Some targeted microbes can fail to amplify due to primer-targeted sequence divergence and be omitted from obtained sequences, leading to differences among primer pairs in the sequenced organisms even when targeting the same community. This potential source of taxonomic bias in HTS makes it prudent to investigate how primer choice will affect the sequenced community prior to investing in a costly community-wide sequencing effort. Here, we use Fluidigm's microfluidic Access Arrays (IFC) followed by Illumina(®) MiSeq Nano sequencing on a culture-derived local mock community to demonstrate how this approach allows for a low-cost combinatorial investigation of primer pairs and experimental samples (up to 48 primer pairs and 48 samples) to determine the most effective primers that maximize obtained communities whilst minimizing taxonomic biases.

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Analyses of ITS and LSU gene regions provide congruent results on fungal community responses

Cited by 45 publications

References 15 publications

Aquatic hyphomycetes in a changing environment

Aquatic hyphomycetes in a changing environment

Scraping the bottom of the barrel: are rare high throughput sequences artifacts?

Don't put all your eggs in one basket: a cost‐effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array

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