The Ecology and Evolution of Pangenomes

Current Biology, Journal Year: 2019, Volume and Issue: 29(20), P. R1094 - R1103

Published: Oct. 1, 2019

Language: Английский

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Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications

Trends in Genetics, Journal Year: 2019, Volume and Issue: 36(2), P. 132 - 145

Published: Dec. 24, 2019

Language: Английский

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Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

Genome biology, Journal Year: 2020, Volume and Issue: 21(1)

Published: Nov. 10, 2020

Abstract Background The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive resilient to biotic abiotic stressors causing recurrent massive mortalities in other bivalves. Although these traits have been recently linked with the maintenance of a high genetic variation within natural populations, factors underlying evolutionary success this species remain unclear. Results Here, after assembly 1.28-Gb reference genome resequencing 14 individuals from two independent we reveal complex pan-genomic architecture M. , core set 45,000 genes plus strikingly number dispensable (20,000) subject presence-absence variation, which may be entirely missing several individuals. We show that are associated hemizygous genomic regions affected by structural variants, overall account for nearly 580 Mb DNA sequence not included assembly. As such, first study report widespread occurrence gene at whole-genome scale animal kingdom. Conclusions Dispensable usually belong young expanded families enriched survival functions, might key explain resilience invasiveness species. This unique pan-genome characterized accessory exceed orders magnitude those observed metazoans, including humans, closely mirror open pan-genomes found prokaryotes few non-metazoan eukaryotes.

Language: Английский

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Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(8), P. 1390 - 1399

Published: July 31, 2023

Pangenomes provide access to an accurate representation of the genetic diversity species, both in terms sequence polymorphisms and structural variants (SVs). Here we generated Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) comprising reference-quality genomes for 142 strains representing species' phylogenetic ecological diversity. The ScRAP includes phased haplotype assemblies several heterozygous diploid polyploid isolates. We identified circa (ca.) 4,800 nonredundant SVs that a broad view genomic diversity, including dynamics telomere length transposable elements. uncovered frequent cases complex aneuploidies where large chromosomes underwent deletions translocations. found can impact gene expression near breakpoints substantially contribute repertoire evolution. also discovered horizontally acquired regions insert at chromosome ends generate new telomeres. Overall, demonstrates benefit pangenome understanding genome evolution population scale.

Language: Английский

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A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici

BMC Biology, Journal Year: 2020, Volume and Issue: 18(1)

Published: Feb. 11, 2020

Abstract Background The gene content of a species largely governs its ecological interactions and adaptive potential. A is therefore defined by both core genes shared between all individuals accessory segregating presence-absence variation. There growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in content. However, it remains unknown how functionally relevant such pangenome structure for eukaryotes what mechanisms underlie the emergence highly polymorphic genome structures. Results Here, we establish reference-quality fungal pathogen wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses production due rapidly evolved tolerance fungicides evasion host resistance. We performed transcriptome-assisted annotations each construct global pangenome. Major chromosomal rearrangements are within extensive Conserved orthogroups account only ~ 60% Investigating functions, find enriched pathogenesis-related functions encodes involved metabolite production, tissue degradation manipulation immune system. De novo transposon annotation shows diverse tightly associated with transposable element Furthermore, expansions likely recent species. Conclusions Taken together, our work establishes complex eukaryotic providing an unprecedented toolbox study impacts crop-pathogen interactions.

Language: Английский

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Fungal evolution: cellular, genomic and metabolic complexity

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2020, Volume and Issue: 95(5), P. 1198 - 1232

Published: April 17, 2020

The question of how phenotypic and genomic complexity are inter-related they shaped through evolution is a central in biology that historically has been approached from the perspective animals plants. In recent years, however, fungi have emerged as promising alternative system to address such questions. Key their ecological success, present broad diverse range traits. Fungal cells can adopt many different shapes, often within single species, providing them with great adaptive potential. cellular organizations span unicellular forms complex, macroscopic multicellularity, multiple transitions higher or lower levels occurring throughout evolutionary history fungi. Similarly, fungal genomes very architecture. Deep changes genome organization occur quickly, these phenomena known mediate rapid adaptations environmental changes. Finally, biochemical huge, particularly regard secondary metabolites, chemical products aspects biology, including interactions. Herein, we explore interplay cellular, metabolic traits mediates emergence complex phenotypes, this Fungi.

Language: Английский

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Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection

Nature Microbiology, Journal Year: 2021, Volume and Issue: 6(12), P. 1526 - 1536

Published: Nov. 24, 2021

Language: Английский

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Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: March 3, 2021

Microbial eukaryotes are found alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes. While critical to these communities, they challenging study with shotgun sequencing techniques therefore often excluded.

Language: Английский

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Facilitators of adaptation and antifungal resistance mechanisms in clinically relevant fungi

Fungal Genetics and Biology, Journal Year: 2019, Volume and Issue: 132, P. 103254 - 103254

Published: July 18, 2019

Opportunistic fungal pathogens can cause a diverse range of diseases in humans. The increasing rate infections caused by strains that are resistant to commonly used antifungals results difficulty treat diseases, with accompanying high mortality rates. Existing and newly emerging molecular resistance mechanisms rapidly spread populations need be monitored. Fungi exhibit diversity maintain physiological resilience create genetic variation; processes which eventually lead the selection pathogens. To prevent anticipate this dispersion, role evolutionary factors drive adaptation should investigated. In review, we provide an overview against antifungal compounds clinic for has been reported. Furthermore, aim summarize elucidate potent generators variability across kingdom aid stressful environments. This knowledge recognizing potential niches facilitate fast development leads new management strategies battle environment.

Language: Английский

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Long reads and Hi‐C sequencing illuminate the two‐compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis

New Phytologist, Journal Year: 2021, Volume and Issue: 233(3), P. 1097 - 1107

Published: Nov. 7, 2021

Summary Chromosome folding links genome structure with gene function by generating distinct nuclear compartments and topologically associating domains. In mammals, these undergo preferential interactions regulate expression. However, their role in fungal biology is unclear. Here, we combine Nanopore (ONT) sequencing chromatin conformation capture (Hi‐C) to reveal chromosome epigenetic diversity a group of obligate plant symbionts: the arbuscular mycorrhizal fungi (AMF). We find that five phylogenetically strains model AMF Rhizophagus irregularis carry 33 chromosomes substantial within‐species variability size, as well repeat content. Strain‐specific Hi‐C contact maps ‘checkerboard’ pattern underline two dominant euchromatin (A) heterochromatin (B) compartments. Each compartment differs level transcription, regulation candidate effectors methylation frequencies. The A‐compartment more gene‐dense contains most core genes, while B‐compartment repeat‐rich has higher rates chromosomal rearrangement. While transcriptionally repressed, it significantly secreted proteins planta upregulated effectors, suggesting possible host‐induced change conformation. Overall, this study provides fine‐scale view into evolution symbionts, opens avenues mechanisms modify during host–microbe interactions.

Language: Английский

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