Subtopic Deep Dive

Phylogenetic Analysis of Yeasts
Research Guide

What is Phylogenetic Analysis of Yeasts?

Phylogenetic analysis of yeasts reconstructs evolutionary relationships using multi-gene phylogenies, phylogenomics, ITS regions, and D1/D2 rDNA sequences to address deep divergences, convergence, and cryptic speciation.

This subtopic applies markers like ITS1, ITS2, and 26S rDNA D1/D2 domains for yeast taxonomy and systematics. Key studies include Fell et al. (2000) analyzing 337 basidiomycetous yeast strains (896 citations) and Satoh et al. (2009) describing Candida auris via D1/D2 and ITS sequencing (1266 citations). Over 10 high-citation papers from 1998-2018 advance fungal yeast phylogenies.

Curated Papers

Key Challenges

Why It Matters

Phylogenetic analysis identifies novel species like Candida auris (Satoh et al., 2009), informing clinical diagnostics and outbreak tracking. It reveals biodiversity patterns in basidiomycetous yeasts (Fell et al., 2000), aiding ecological studies and biotech strain selection. Genome-scale phylogenies like Peter et al. (2018) on 1,011 Saccharomyces cerevisiae isolates trace trait evolution, supporting fermentation industry improvements and evolutionary biology insights.

Key Research Challenges

ITS Region Sequence Processing

Extracting accurate ITS1 and ITS2 from noisy environmental sequences remains difficult despite tools like those in Bengtsson-Palme et al. (2013, 1351 citations). Variations in primer efficiency, as tested by Ihrmark et al. (2012, 2030 citations), affect community analyses. This leads to biased yeast diversity estimates in metagenomic data.

Resolving Cryptic Speciation

Multi-gene phylogenies struggle to differentiate cryptic yeast species, as seen in Candida auris identification (Satoh et al., 2009, 1266 citations). D1/D2 domain analysis helps but requires phylogenomic integration (Fell et al., 2000). Deep divergences confound tree reconstructions without whole-genome data.

Primer Coverage for Yeasts

Standard ITS primers miss ascomycete and basidiomycete yeasts in samples, addressed by Toju et al. (2012, 1207 citations). Coverage gaps persist across yeast subphyla. High-throughput sequencing demands robust, broad-spectrum primers for accurate phylogenies.

Essential Papers

The Top 10 fungal pathogens in molecular plant pathology

Ralph A. Dean, J.A.L. van Kan, Z. A. Pretorius et al. · 2012 · Molecular Plant Pathology · 4.4K citations

SUMMARY The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place ...

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

Katarina Ihrmark, Inga T. M. Bödeker, Karelyn Cruz-Martínez et al. · 2012 · FEMS Microbiology Ecology · 2.0K citations

With recent methodological advances, molecular markers are increasingly used for semi-quantitative analyses of fungal communities. The aim to preserve quantitative relationships between genotypes t...

Improved software detection and extraction of ITS1 and <scp>ITS</scp> 2 from ribosomal <scp>ITS</scp> sequences of fungi and other eukaryotes for analysis of environmental sequencing data

Johan Bengtsson‐Palme, Martin Ryberg, Martin Hartmann et al. · 2013 · Methods in Ecology and Evolution · 1.4K citations

Summary The nuclear ribosomal internal transcribed spacer ( ITS ) region is the primary choice for molecular identification of fungi. Its two highly variable spacers ( ITS 1 and ITS 2) are usually ...

<i>Candida auris</i>sp. nov., a novel ascomycetous yeast isolated from the external ear canal of an inpatient in a Japanese hospital

Kazuo Satoh, Koichi Makimura, Yayoi Hasumi et al. · 2009 · Microbiology and Immunology · 1.3K citations

ABSTRACT A single strain of a novel ascomycetous yeast species belonging to the genus Candida was isolated from the external ear canal of an inpatient in a Japanese hospital. Analyses of the 26S rD...

High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples

Hirokazu Toju, Akifumi S. Tanabe, Satoshi Yamamoto et al. · 2012 · PLoS ONE · 1.2K citations

The kingdom Fungi is estimated to include 1.5 million or more species, playing key roles as decomposers, mutualists, and parasites in every biome on the earth. To comprehensively understand the div...

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

Ignazio Verde, Albert G. Abbott, Simone Scalabrin et al. · 2013 · Nature Genetics · 1.2K citations

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

Jackson Peter, Matteo De Chiara, Anne Friedrich et al. · 2018 · Nature · 1.2K citations

Reading Guide

Foundational Papers

Start with Fell et al. (2000) for basidiomycetous yeast D1/D2 systematics (896 citations), then Satoh et al. (2009) for ascomycete ITS/D1/D2 species description, and Ihrmark et al. (2012) for ITS2 primer evaluation.

Recent Advances

Study Peter et al. (2018) for Saccharomyces phylogenomics across 1,011 isolates and Bengtsson-Palme et al. (2013) for ITS processing software improvements.

Core Methods

Core techniques: D1/D2 rDNA sequencing (Fell et al., 2000), ITS primer amplification (Toju et al., 2012; Ihrmark et al., 2012), sequence extraction software (Bengtsson-Palme et al., 2013), and multi-locus phylogenies.

How PapersFlow Helps You Research Phylogenetic Analysis of Yeasts

Discover & Search

Research Agent uses searchPapers and exaSearch to find ITS-focused yeast papers like Bengtsson-Palme et al. (2013), then citationGraph reveals connections to Fell et al. (2000) and Satoh et al. (2009). findSimilarPapers expands to phylogenomic studies from Peter et al. (2018).

Analyze & Verify

Analysis Agent applies readPaperContent to extract D1/D2 sequences from Satoh et al. (2009), verifies phylogenetic claims with CoVe against Ihrmark et al. (2012), and runs PythonAnalysis for sequence alignment stats using NumPy/pandas. GRADE scores evidence strength for ITS primer reliability.

Synthesize & Write

Synthesis Agent detects gaps in cryptic speciation coverage across Fell et al. (2000) and Toju et al. (2012), flags contradictions in primer performance. Writing Agent uses latexEditText, latexSyncCitations for phylogeny manuscripts, and latexCompile for publication-ready outputs with exportMermaid for evolutionary trees.

Use Cases

"Analyze ITS sequence alignment from environmental yeast samples for phylogenetic tree building."

Research Agent → searchPapers('yeast ITS phylogeny') → Analysis Agent → runPythonAnalysis(NumPy dendropy tree plot, pandas alignment stats) → matplotlib tree visualization output.

"Draft LaTeX figure of D1/D2 phylogeny for Candida auris paper."

Analysis Agent → readPaperContent(Satoh 2009) → Synthesis Agent → gap detection → Writing Agent → latexGenerateFigure + latexSyncCitations + latexCompile → compiled PDF with yeast tree diagram.

"Find GitHub code for fungal ITS primer design from recent papers."

Research Agent → searchPapers('ITS primers yeasts') → Code Discovery → paperExtractUrls(Toju 2012) → paperFindGithubRepo → githubRepoInspect → primer optimization Python scripts.

Automated Workflows

Deep Research workflow scans 50+ papers on yeast ITS/D1/D2 markers (e.g., Ihrmark et al. 2012 → Bengtsson-Palme et al. 2013), producing structured phylogeny review with GRADE scores. DeepScan applies 7-step verification: search → read → Python alignment → CoVe → synthesis → LaTeX → critique for robust yeast tree analysis. Theorizer generates hypotheses on convergence from Peter et al. (2018) genomes linked to Fell et al. (2000).

Try Doxa for Phylogenetic Analysis of Yeasts Research

Frequently Asked Questions

What defines phylogenetic analysis of yeasts?

It reconstructs evolutionary trees using ITS regions, D1/D2 rDNA, and multi-gene data to resolve divergences and speciation in ascomycetous and basidiomycetous yeasts.

What are key methods in yeast phylogenetics?

Methods include ITS1/ITS2 sequencing with primers (Ihrmark et al., 2012; Toju et al., 2012), D1/D2 domain analysis (Fell et al., 2000; Satoh et al., 2009), and phylogenomics (Peter et al., 2018).

What are major papers on yeast phylogenies?

Foundational works: Fell et al. (2000, 896 citations) on basidiomycetous yeasts; Satoh et al. (2009, 1266 citations) on Candida auris. Recent: Peter et al. (2018, 1158 citations) on Saccharomyces genomes.

What open problems exist?

Challenges include ITS extraction accuracy (Bengtsson-Palme et al., 2013), resolving cryptic species beyond D1/D2, and primer biases for diverse yeast lineages in metagenomes.