ArticleGenome biology and evolution2020
What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen.
Article in Genome biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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
28 citing papers in PubMed, 53 citations in OpenAlex.
- The Impact of Visible Symptoms of Thallus Damage on the Phycobiota of Mediterranean Epiphytic Lichens.Microbial ecology · 2026Article
- Chloroplast and Mitochondrial Genomes of the Lichen-Symbiotic Green Alga Trebouxia Illuminate Evolutionary Relationships and Climate Associations and Yield New Phylogenetic Markers.Genome biology and evolution · 2026Article
- Convergent symbioses: morphology, life history, and niche specialization in coral and lichen mutualisms.FEMS microbiology reviews · 2026Review
- Chromosome-level genome assembly of the photobiont microalga Trebouxia sp. 'A48' from the lichen Xanthoria parietina.The New phytologist · 2026Article
- A reference metagenome sequence of the lichen Cladonia rangiformis.BMC biology · 2025Article
- Evaluating the Assembly Strategy of a Fungal Genome from Metagenomic Data:Journal of fungi (Basel, Switzerland) · 2025Article
- Microbial occurrence and symbiont detection in a global sample of lichen metagenomes.PLoS biology · 2024Article
- Genome-Wide Comparisons Reveal Extensive Divergence Within the Lichen Photobiont Genus, Trebouxia.Genome biology and evolution · 2024Article
- Microbiomic Analysis of Bacteria Associated with Rock Tripe Lichens from Alpine Areas in Eastern Alps and Equatorial Africa.Current microbiology · 2024Article
- Bacteriomic Profiles of Rock-Dwelling Lichens from the Venezuelan Guiana Shield and the South African Highveld Plateau.Microorganisms · 2024Article
- Reclassification of Botryococcus braunii chemical races into separate species based on a comparative genomics analysis.PloS one · 2024Article
- Bacterial phylotypes associated with rock-dwellingPolar biology · 2024Article
- Article
- MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes.Scientific data · 2023Article
- The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution.Communications biology · 2023Article
- The reference genome assembly of the bright cobblestone lichen, Acarospora socialis.The Journal of heredity · 2023Article
- Genome-Wide Analysis of the Cytochrome P450 Monooxygenases in the Lichenized Fungi of the ClassMicroorganisms · 2023Article
- Biosynthetic gene cluster synteny: Orthologous polyketide synthases in Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata.MicrobiologyOpen · 2023Article
- Biosynthetic Potential ofJournal of fungi (Basel, Switzerland) · 2023Article
- First Whole Genome Sequence and Flow Cytometry Genome Size Data for the Lichen-Forming Fungus Ramalina farinacea (Ascomycota).Genome biology and evolution · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis-the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)-were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ∼20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long 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.