ArticleScientific reports2017
Reference-based RADseq resolves robust relationships among closely related species of lichen-forming fungi using metagenomic DNA.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity.International journal of molecular sciences · 2019Pooled it
- Unravelling the Secret of Phantom Phenotypes in Macrolichens: Insights From Cladonia bellidiflora Complex.Molecular ecology · 2026Article
- High-Throughput Sequencing Supports Strong Geographical Patterns in theJournal of fungi (Basel, Switzerland) · 2026Article
- UnFATE: A Comprehensive Probe Set and Bioinformatics Pipeline for Phylogeny Reconstruction and Multilocus Barcoding of Filamentous Ascomycetes (Ascomycota, Pezizomycotina).Systematic biology · 2025Article
- Reference-Based Restriction-Site-Associated DNA Sequencing Data Are Useful for Species Delineation in a Recently Diverged Asexually Reproducing Species Complex (Parmeliaceae, Ascomycota).Journal of fungi (Basel, Switzerland) · 2023Article
- Reference-Based RADseq Unravels the Evolutionary History of Polar Species in 'the Crux Lichenologorum' GenusJournal of fungi (Basel, Switzerland) · 2023Article
- Article
- Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M.Genome biology · 2022Article
- Species boundaries in the messy middle-A genome-scale validation of species delimitation in a recently diverged lineage of coastal fog desert lichen fungi.Ecology and evolution · 2021Article
- Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing.BMC genomics · 2021Article
- Towards a Natural Classification ofJournal of fungi (Basel, Switzerland) · 2021Article
- An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota.Life (Basel, Switzerland) · 2020Review
- Genome-scale data reveal the role of hybridization in lichen-forming fungi.Scientific reports · 2020Article
- Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi.BMC evolutionary biology · 2020Article
- Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?IMA fungus · 2020Article
- Article
- Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota).Scientific reports · 2019Article
- Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal speciesMycoKeys · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite increasing availability of phylogenomic datasets, strategies to generate genome-scale data from organisms involved in symbiotic relationships remains challenging. Restriction site-associated DNA sequencing (RADseq) can effectively generated reduced representation genomic loci. However, when using metagenomic DNA from inseparable symbiotic organisms, RADseq loci may belong to any number of the organisms involved in these intimate associations. In this study, we explored the potential for a reference-based RADseq approach to generate data for lichen-forming fungi from metagenomic DNA extracted from intact lichens. We simulated RAD data from draft genomes of closely related lichenized fungi to test if RADseq can reconstruct robust evolutionary relationships. Subsequently, we generated empirical RADseq data from metagenomic lichen DNA, with RADseq loci mapped back to a reference genome to exclude loci from other lichen symbionts that are represented in metagenomic libraries. In all cases, phylogenetic reconstructions using RADseq loci recovered diversification histories consistent with a previous study based on more comprehensive genome sampling. Furthermore, RADseq loci were found to resolve relationships among closely related species, which were otherwise indistinguishable using a phylogenetic species recognition criterion. Our studies revealed that a modified, reference-based RADseq approach can successfully be implemented to generate symbiont-specific phylogenomic data from metagenomic reads.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.