Using Gap Visualization to Navigate Multivariate Metabarcode Data, Select Primer Pairs, and Enhance Reference Data Quality DOI Creative Commons
Xin‐Yi Chua,

Louise Ord,

Stephen J. Bent

et al.

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(6)

Published: Nov. 1, 2024

ABSTRACT The success of amplicon sequencing studies environmental DNA (eDNA) depends on the choice primer pairs used to select taxa‐specific regions for amplification then characterize sample composition. This paper presents practical methods visualize extent which different can differentiate taxonomic groups, enabling researchers assess primers might be best suited a study or environment interest. These also review annotations in genomic reference sequence databases. We apply concept barcoding gaps metabarcoding multiple species leverage data sequences previously characterized specimens. Since sets are large and complex, we provide simple intuitive method navigate subsets containing conflicting ambiguous relationships between information classification. demonstrate how use gap visualization segmentation comparing well discriminate interest, detecting anomalies annotation. show these enable survey design make fundamental molecular resources more accessible wider research audience beyond bioinformaticians scientists.

Language: Английский

Role of Fungi in Tumorigenesis: Promises and Challenges DOI
Silvia Guglietta, Xin Li, Deepak Saxena

et al.

Annual Review of Pathology Mechanisms of Disease, Journal Year: 2025, Volume and Issue: 20(1), P. 459 - 482

Published: Jan. 24, 2025

The mycobiome plays a key role in the host immune responses homeostasis and inflammation. Recent studies suggest that an imbalance gut's fungi contributes to chronic, noninfectious diseases such as obesity, metabolic disorders, cancers. Pathogenic can colonize specific organs, gut has been linked development progression of various cancers, including colorectal, breast, head neck, pancreatic Some fungal species promote tumorigenesis by triggering complement system. However, immunocompromised patients, also inhibit this activation establish life-threatening infections. Interestingly, interaction bacteria induce unique responses. breakthroughs advancements high-throughput sequencing tumor mycobiomes are highlighting novel diagnostic therapeutic opportunities for cancer. We discuss latest developments field cancer potential benefits challenges antifungal therapies.

Language: Английский

Citations

1
Protein Coding Low‐Copy rpb2 and ef1‐α Regions Are Viable Fungal Metabarcoding DNA Markers Which Can Supplement ITS for Better Accuracy DOI Creative Commons
Vasilii Shapkin, Miroslav Caboň, Miroslav Kolařík

et al.

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

ABSTRACT The nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region is used as a universal fungal barcode marker, but often lacks significant barcoding gap between sister taxa. Here we tested the reliability of protein coding low‐copy genes alternative markers. Mock communities three unrelated agaric genera ( Dermoloma , Hodophilus and Russula ) representing lineages closely related species were sequenced by Illumina platform targeting ITS1, ITS2, second largest subunit RNA polymerase II gene rpb2 transcription elongation factor 1‐alpha ef1‐α regions. Species representation their relative abundances similar across all regions, despite lower copy number in ITS1 ITS2 required more sophisticated sequence filtering because they produced high chimeric sequences requiring reference‐based chimera removal had higher variants per species. Although clustering filtered ITS resulted an average correctly clustered units at optimal similarity thresholds, these thresholds varied substantially among genera. Best‐fitted markers consistent frequently lacked resolution due to low intraspecific variability. At some observed multiple lumped together, same time, split into partial clusters, which should be taken consideration when assessing best taxonomic identity clusters. To achieve improve detection, recommend combining different applying additional sorting current availability reference public databases far from being complete for groups, combined marker approach can group‐specific studies that build data own purposes.

Language: Английский

Citations

0
Morphological, phylogenetic, and genomic evidence reveals the causal agent of thread blight disease of cacao in Peru is a new species of Marasmius in the section Neosessiles, Marasmius infestans sp. nov. DOI Creative Commons
Ángel Fernando Huaman-Pilco, Tito Ademir Ramos-Carrasco, Mario Emilio Ernesto Franco

et al.

F1000Research, Journal Year: 2024, Volume and Issue: 12, P. 1327 - 1327

Published: Jan. 29, 2024

The thread blight disease (TBD) of cacao (Theobroma cacao) in the department Amazonas, Peru was recently reported to be caused by Marasmius tenuissimus (sect. Neosessiles). This same species is known main causal agent TBD West Africa. However, some morphological characteristics, such as presence rhizomorphs, almost exclusively white color, and pileus sizes less than 5 mm, among others, differ description M. tenuissimus. Therefore, we aimed conduct a taxonomic revision cacao-TBD Peru, using thorough micro macro morphological, phylogenetic, nuclear mitochondrial genomic approaches. We showed that belongs new species, infestans sp. nov. study enriches our knowledge sect. Neosessiles, strongly suggests complex highly diverse.

Language: Английский

Citations

2
Ectomycorrhizal fungi are influenced by ecoregion boundaries across Europe DOI
Guillaume Delhaye, Sietse van der Linde, D.E. Bauman

et al.

Global Ecology and Biogeography, Journal Year: 2024, Volume and Issue: 33(6)

Published: April 5, 2024

Abstract Aim Ecoregions and the distance decay in community similarity are fundamental concepts biogeography conservation biology that well supported across plants animals, but not fungi. Here we test relevance of these for ectomycorrhizal (ECM) fungi temperate boreal regions. Location Europe. Time Period 2008–2015. Major Taxa Studied Ectomycorrhizal Methods We used a large dataset ~24,000 ectomycorrhizas, assigned to 1350 operational taxonomic units, collected from 129 forest plots via standardized protocol. investigated ecoregion delimitations ECM through complementary methodological approaches based on models, multivariate analyses indicator species analyses. then evaluated effects host tree climate observed biogeographical distributions. Results predict large‐scale fungal biodiversity patterns. This is partly explained by differences between ecoregions independent distribution. Basidiomycetes orders Russulales Atheliales producing epigeous fruiting bodies, with potentially short‐distance dispersal, show best agreement boundaries. Host distribution abundance (as opposed presence/absence only) important uncover patterns mycorrhizas. Main Conclusions useful units investigate eco‐evolutionary processes mycorrhizal communities decision‐making includes

Language: Английский

Citations

2
Diaporthe species on palms – integrative taxonomic approach for species boundaries delimitation in the genus Diaporthe, with the description of D. pygmaeae sp. nov. DOI
Diana S. Pereira, Alan J. L. Phillips

Studies in Mycology, Journal Year: 2024, Volume and Issue: 109(1), P. 487 - 594

Published: Oct. 24, 2024

Language: Английский

Citations

2
How to best detect threatened deadwood fungi – Comparing metabarcoding and fruit body surveys DOI
Daniel Rieker, Kadri Runnel,

Petr Baldrian

et al.

Biological Conservation, Journal Year: 2024, Volume and Issue: 296, P. 110696 - 110696

Published: July 11, 2024

Language: Английский

Citations

1
What Quality Suffices for Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in Decaying Fagus sylvatica Bark as Case Study DOI Creative Commons
Glen Dierickx, Lowie Tondeleir, Pieter Asselman

et al.

Journal of Fungi, Journal Year: 2024, Volume and Issue: 10(10), P. 708 - 708

Published: Oct. 10, 2024

Nanopore raw read accuracy has improved to over 99%, making it a potential tool for metabarcoding. For broad adoption, guidelines on quality filtering are needed ensure reliable taxonomic unit recovery. This study aims provide those fungal metabarcoding context and apply them case of ectomycorrhizae in the decaying bark

Language: Английский

Citations

1
Integrating DNA Barcoding Within an Orthogonal Approach for Herbal Product Authentication: A Narrative Review DOI Creative Commons
Nazia Nazar,

Akanksha Saxena,

Aimy Sebastian

et al.

Phytochemical Analysis, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 12, 2024

ABSTRACT Introduction Existing methods for morphological, organoleptic, and chemical authentication may not adequately ensure the accurate identification of plant species or guarantee safety. Herbal raw material remains a major challenge in herbal medicine. Over past decade, DNA barcoding, combined with an orthogonal approach integrating various testing quality assurance, has emerged as new trend authentication. Objective The review evaluates barcoding common alternative plant‐related sectors to enhance assurance Method Studies were selected based on their relevance identification, safety products. Inclusion criteria peer‐reviewed articles, systematic reviews, relevant case studies from last two decades focused methods, applications. Exclusion involved lacking empirical data, those peer‐reviewed, unrelated main focus. This ensured inclusion high‐quality, pertinent sources while excluding less studies. Results An refers use multiple, independent that provide complementary information more assurance. reduces false positives negatives by confirming results through different techniques, combining morphological analysis profiling. It enhances confidence results, particularly cases potential adulteration misidentification materials. Conclusion study highlights persistent challenges assuring quality, purity, Additionally, it stresses importance incorporating DNA‐based alongside traditional identification.

Language: Английский

Citations

1
Ectomycorrhizal fungi are influenced by ecoregion boundaries across Europe DOI Creative Commons
Guillaume Delhaye, Sietse van der Linde, D.E. Bauman

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 11, 2024

Abstract Aim Ecoregions and the distance decay in community similarity are fundamental concepts biogeography conservation biology that well supported across plants animals, but not fungi. Here we test relevance of these for ectomycorrhizal (ECM) fungi temperate boreal regions. Location Europe. Time period 2008 – 2015. Major taxa studied Ectomycorrhizal Methods We used a large dataset ∼ 24,000 ectomycorrhizas, assigned to 1,350 operational taxonomic units, collected from 129 forest plots via standardised protocol. investigated ecoregion delimitations ECM through complementary methodological approaches based on models, multivariate analyses, indicator species analyses. then evaluated effects host tree climate observed biogeographical distributions. Results predict large-scale fungal biodiversity patterns. This is partly explained by differences between ecoregions independent distribution. Basidiomycetes orders Russulales Atheliales producing epigeous fruiting bodies, with potentially short-distance dispersal, show best agreement boundaries. Host distribution abundance (as opposed presence/absence only) important uncover patterns mycorrhizas. Main conclusions useful units investigate eco-evolutionary processes mycorrhizal communities decision-making includes

Language: Английский

Citations

0
What Quality Suffices in Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in Decaying Fagus sylvatica Bark as a Case-Study DOI Open Access
Glen Dierickx, Lowie Tondeleir, Pieter Asselman

et al.

Published: Aug. 29, 2024

Nanopore raw read accuracy has improved to over 99%, making it a potential tool for metabarcoding. For broad adoption, guidelines on quality filtering are needed ensure reliable taxonomic unit recovery. This study aims provide those fungal metabarcoding context and apply them case-study of ectomycorrhizae in decaying bark Fagus sylvatica.We introduce the eNano pipeline test two standard approaches: (1) reference-based mapping leveraging UNITE’s species hypothesis system (SH-approach) (2) constructing 98% OTUs (OTU-approach). We evaluate these approaches using mock natural community. Our results demonstrate that both effective with data. When reference database, we recommend strict criteria rather than Phred-based filtering. OTUs, reads at ≥Q25 is recommended. reveals decay gradient primary determinant community composition, specific mycorrhizal fungi colonize bark. Complementing our root tip morphotypification, identify Laccaria amethystina Tomentella sublilacina as key saplings logs. These findings sequencing can valuable ecological insights support its broader use continues improve.

Language: Английский

Citations

0