Biodiversity
Aspergillus genomic diversity
Open access · cc by · source: Europe PMC
Comparative genomics shows Aspergillus species share genome size but harbor large lineage-specific gene sets.
How this study connects
Role on claims
Each row is a claim on a concept or method page where this paper supports, challenges, or qualifies the statement. Roles are hand-checked — not a model guess.
Aspergillus clade genomics and a Listeria pan-genome reassessment use trees and gene-content matrices together. Aspergillus genomes were ~29–36 Mb with 9,113–13,553 genes, about 20% Aspergillaceae-specific, and section Nigri averaged ~1,800 unique genes. Extending L. monocytogenes by 11 strains covering all serotypes showed a highly stable but not closed pan-genome, with accessory genes in hypervariable hotspots and mobile elements as major accessory components.
Evidence for the claim as stated.
What 'accessory' or 'lineage-specific' genes imply is itself unsettled. Listeria accessory genes concentrate in hotspots with mobile elements and aid diagnostics, but presence/absence does not prove each virulence phenotype. Aspergillus section Nigri's ~1,800 unique genes are not experimentally validated one by one. Immune-gene sharing of selection between birds and mammals can be convergence or ancient pressure.
Evidence for the claim as stated.
Three papers are false-positive lexicon hits for proteomics. Naegleria fowleri work assembled an ~30 Mb AT-rich genome and listed candidate pathogenicity genes; Aspergillus comparative genomics reported ~29–36 Mb genomes with 9,113–13,553 genes (~20% Aspergillaceae-specific; section Nigri ~1,800 unique genes); Plasmodium falciparum IDC transcriptome was hourly expression across a ~48-hour blood-stage cycle. Those are DNA or RNA catalogues, not peptide spectra.
Evidence for the claim as stated.
Naegleria and Aspergillus genomes and the Plasmodium IDC transcriptome should not be cited as mass-spectrometry evidence at all. Candidate pathogenicity gene lists and periodic RNA profiles are sequence resources that still need protein-level or infection-model tests.
Evidence for the claim as stated.
Open questions
Tensions this paper is part of
From concept pages' “where studies disagree.” Disagreement means the same question; scope means different assays, populations, or outcomes.
What 'accessory' or 'lineage-specific' genes imply is itself unsettled. Listeria accessory genes concentrate in hotspots with mobile elements and aid diagnostics, but presence/absence does not prove each virulence phenotype. Aspergillus section Nigri's ~1,800 unique genes are not experimentally validated one by one. Immune-gene sharing of selection between birds and mammals can be convergence or ancient pressure.
- Supports · How open is the Listeria pan-genome?
- Supports · Why do immune genes keep evolving across tetrapods?
Naegleria and Aspergillus genomes and the Plasmodium IDC transcriptome should not be cited as mass-spectrometry evidence at all. Candidate pathogenicity gene lists and periodic RNA profiles are sequence resources that still need protein-level or infection-model tests.
Study at a glance
- Design
- Computational / modelling — Comparative genomics of Aspergillus genomes in MycoCosm
- N
- Multi-genome Aspergillus comparison (≈29–36 Mb; 9,113–13,553 genes) — genome count not a single primary N in stored summary
- Population
- Aspergillus / Aspergillaceae genomes
- Outcome
- Genome size, gene content, and clade-specific gene expansions
Structured fields used in claim comparison tables when every cited study has a complete layer.
Inspect source passages
Aspergillus genomic diversity
These passages occur verbatim in the stored paper text. They support the points listed below; they do not verify every statement in the explanation.
Predicted genes 9113–13,553.
The number of predicted genes in the aspergilli is in the range of 9113–13,553, which is generally higher than that observed for the Onygenales (<10,000; Additional file B).
About 20% genes specific to Aspergillaceae.
A substantial proportion (80% on average) of the identified genes in Aspergillaceae genomes have homologs in other lineages of fungi, indicating that around 20% are specific to Aspergillaceae.
Key findings
Genomes ~29–36 Mb with 9,113–13,553 genes; ~20% Aspergillaceae-specific; section Nigri averages ~1,800 unique genes.
Methodology
Compared Aspergillus genomes in MycoCosm for size, GC, gene content, repeats, and clade-specific genes.
Limitations
Does not experimentally validate every lineage-specific gene’s phenotype.
Related papers in this topic
Same topic cluster — not a recommendation engine.