ArticleBMC genomics2025
Ancestral and recent bursts of transposition shaped the massive genomes of plant pathogenic rust fungi.
Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 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
3 citing papers in PubMed.
- Haplotype-phased genomes of the barley leaf rust pathogen reveal evidence of repeat element expansion and somatic hybridization.G3 (Bethesda, Md.) · 2026Article
- TrichoBase: a standardized genomic resource for comparative genomics of Trichoderma species.BMC genomic data · 2026Article
- Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus.Genome research · 2025Article
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
backgroundTransposable elements (TEs) play a crucial role in genome evolution, influencing gene regulation, diversity, and genome architecture. Rust fungi of the order Pucciniales (Subphylum Pucciniomycotina) are the largest group of obligate biotrophic plant pathogens and harbor some of the largest and most TE-rich genomes-up to 1.2 Gb-compared to other fungi. This global genomic expansion contrasts with the smaller genomes and minimal mobilome found in other Pucciniomycotina species. Despite the availability of high-quality genome assemblies, our understanding of TE dynamics in Pucciniales remains limited due to inconsistent and incomplete TE annotations.
resultsWe analyzed the mobilomes of 12 Pucciniomycotina species, producing a manually curated TE library for each genome. In Pucciniales, TEs occupy 47-92% of the genome, whereas 2-36% of TEs are detected in other Pucciniomycotina genomes. The comparison of gene and TE repertoires indicates that TEs, particularly LTR-retrotransposons and TIR-DNA transposons, are the primary contributors to the genome expansion of the Pucciniales. We reconstructed the proliferation histories of TEs in the Pucciniales, combining sequence similarity, clustering, and molecular clock approaches. We highlight recent and ancient TE invasions with some LTR-Gypsy elements predating the divergence of Pucciniomycotina (~ 176 Mya), while most TE accumulation in Pucciniales occurred within the last 50 Mya. However, the TE invasions in the Pucciniales genomes do not seem to result from specific deficiencies in known TE-control mechanisms.
conclusionOur findings uncover extensive TE proliferation in Pucciniales, predominantly driven by LTR-Gypsy expansions. The retention of ancestral TEs and the consistently TE-rich genomes observed in Pucciniales highlight TE proliferation as an ancestral genomic feature in rust fungi.
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.