Systematic identification of cargo-mobilizing genetic elements reveals new dimensions of eukaryotic diversity

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(10), P. 5496 - 5513

Published: April 15, 2024

Abstract Cargo-mobilizing mobile elements (CMEs) are genetic entities that faithfully transpose diverse protein coding sequences. Although common in bacteria, we know little about eukaryotic CMEs because no appropriate tools exist for their annotation. For example, Starships giant fungal whose functions largely unknown they require time-intensive manual curation. To address this knowledge gap, developed starfish, a computational workflow high-throughput CME We applied starfish to 2 899 genomes of 1 649 species and found recovers known with 95% combined precision recall while expanding the number annotated ten-fold. Extant Starship diversity is partitioned into 11 families differ enrichment patterns across classes. cargo changes rapidly such from same family substantially functional repertoires, which predicted contribute biological processes as metabolism. Many have convergently evolved insert 5S rDNA AT-rich sequence others integrate random locations, revealing both specialist generalist strategies persistence. Our work establishes framework advancing element biology provides means investigate an emerging dimension diversity, within genomes.

Language: Английский

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Multiple horizontal mini-chromosome transfers drive genome evolution of clonal blast fungus lineages

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(8)

Published: Aug. 1, 2024

Abstract Crop disease pandemics are often driven by asexually reproducing clonal lineages of plant pathogens that reproduce asexually. How these continuously adapt to their hosts despite harboring limited genetic variation, and in absence sexual recombination remains elusive. Here, we reveal multiple instances horizontal chromosome transfer within pandemic the blast fungus Magnaporthe (Syn. Pyricularia) oryzae. We identified a horizontally transferred 1.2Mb accessory mini-chromosome which is remarkably conserved between M. oryzae isolates from both rice lineage infecting Indian goosegrass (Eleusine indica), wild grass grows proximity cultivated cereal crops. Furthermore, show this was acquired through at least nine distinct events over past three centuries. These findings establish as mechanism facilitating exchange among different host-associated lineages. propose populations grasses act reservoirs drive genome evolution afflict

Language: Английский

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Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Abstract Deadwood provides habitat for fungi and serves diverse ecological functions in forests. We already have profound knowledge of fungal assembly processes, physiological enzymatic activities, resulting physico-chemical changes during deadwood decay. However, situ detection identification methods, origins, a mechanistic understanding the main lignocellulolytic enzymes are lacking. This study used metaproteomics to detect extracellular 12 tree species temperate forest that decomposed 8 ½ years. Mainly white-rot (and few brown-rot) Basidiomycota were identified as wood decomposers, with Armillaria dominant genus; additionally, several soft-rot xylariaceous Ascomycota identified. The key involved lignocellulolysis included manganese peroxidase, peroxide-producing alcohol oxidases, laccase, glycoside hydrolases (cellulase, glucosidase, xylanase), esterases, lytic polysaccharide monooxygenases. community enzyme composition differed among species. more prevalent angiosperm logs than gymnosperm logs. Regarding function, toolbox acted simultaneously was interrelated (e.g. peroxidases strongly correlated), highly functionally redundant, present all In summary, our comprehensive detailed insight into machinery wood-inhabiting These findings will allow us relate environmental factors an ecosystem function future.

Language: Английский

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Molecular phylogenetic and estimation of evolutionary divergence and biogeography of the family Schizoparmaceae and allied families (Diaporthales, Ascomycota)

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: unknown, P. 108211 - 108211

Published: Oct. 1, 2024

Language: Английский

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Horizontal transfer of accessory chromosomes in fungi – a regulated process for exchange of genetic material?

Heredity, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 10, 2025

Abstract Horizontal transfer of entire chromosomes has been reported in several fungal pathogens, often significantly impacting the fitness recipient fungus. All documented instances horizontal chromosome transfers (HCTs) showed a marked propensity for accessory chromosomes, consistently involving an while other were seldom, if ever, co-transferred. The mechanisms underlying HCTs, as well factors regulating specificity HCTs remain unclear. In this perspective, we provide overview observed cases transfers. We hypothesize existence signal that distinguishes mobile, i.e., horizontally transferred, from rest donor genome. Recent findings Metarhizium robertsii and Magnaporthe oryzae , suggest mobile may contain putative histones and/or histone modifiers, which could generate such signal. Based on this, propose encode machinery required their own transmission, implying HCT be regulated process. Finally, present evidence substantial differences codon usage bias between core 14 out 19 analysed species strains. Such indicate past these chromosomes. Interestingly, was previously unknown many species, suggesting more widespread than thought, therefore important factor genome evolution.

Language: Английский

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Morphogenesis, starvation, and light responses in a mushroom-forming fungus revealed by long-read sequencing and extensive expression profiling

Cell Genomics, Journal Year: 2025, Volume and Issue: unknown, P. 100853 - 100853

Published: April 1, 2025

Mushroom-forming fungi (Agaricomycetes) are emerging as pivotal players in several fields of science and industry. Genomic data for Agaricomycetes accumulating rapidly; however, this is not paralleled by improvements gene annotations, which leave function notoriously poorly understood. We set out to improve our functional understanding the model mushroom Coprinopsis cinerea integrating a new, chromosome-level assembly, high-quality predictions, information derived from broad gene-expression profiling data. The new annotation includes 5' 3' untranslated regions (UTRs), polyadenylation sites (PASs), upstream open reading frames (uORFs), splicing isoforms, microexons, well core sets corresponding carbon starvation, light response, hyphal differentiation. As result, genome C. has now become most comprehensively annotated among mushroom-forming fungi, will contribute multiple rapidly expanding fields, including research on their life history, stress responses, multicellular development.

Language: Английский

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How genomics can help unravel the evolution of endophytic fungi

World Journal of Microbiology and Biotechnology, Journal Year: 2025, Volume and Issue: 41(5)

Published: April 28, 2025

Language: Английский

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Snowball: a novel gene family required for developmental patterning of fruiting bodies of mushroom-forming fungi (Agaricomycetes)

mSystems, Journal Year: 2024, Volume and Issue: 9(3)

Published: Feb. 9, 2024

The morphogenesis of sexual fruiting bodies fungi is a complex process determined by genetically encoded program. Fruiting reached the highest complexity levels in Agaricomycetes; yet, underlying genetics currently poorly known. In this work, we functionally characterized highly conserved gene termed

Language: Английский

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Lifestyles shape genome size and gene content in fungal pathogens

Published: April 2, 2025

Fungi display a wide range of lifestyles and hosts. We still know little about the impact lifestyles, including pathogenicity, on their genome architecture. Here, we combined annotated 552 fungal genomes from class Sordariomycetes examined association between 12 genomic features two lifestyle traits: pathogenicity insect association. found that pathogens average tend to have larger number protein-coding genes, effectors, tRNA genes. In addition, non-repetitive size is than non-pathogenic species. However, this pattern not consistent across all groups. Insect endoparasites symbionts smaller sizes genes with longer exons; moreover, insect-vectored possess fewer compared those transmitted by insects. Our study shows are main contributors variation in seemingly similar can exhibit distinct architectures, depending host vector interactions.

Language: Английский

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Lifestyles shape genome size and gene content in fungal pathogens

Published: April 2, 2025

Fungi display a wide range of lifestyles and hosts. We still know little about the impact lifestyles, including pathogenicity, on their genome architecture. Here, we combined annotated 552 fungal genomes from class Sordariomycetes examined association between 12 genomic features two lifestyle traits: pathogenicity insect association. found that pathogens average tend to have larger number protein-coding genes, effectors, tRNA genes. In addition, non-repetitive size is than non-pathogenic species. However, this pattern not consistent across all groups. Insect endoparasites symbionts smaller sizes genes with longer exons; moreover, insect-vectored possess fewer compared those transmitted by insects. Our study shows are main contributors variation in seemingly similar can exhibit distinct architectures, depending host vector interactions.

Language: Английский

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