The Ecology and Evolution of Pangenomes

Current Biology, Год журнала: 2019, Номер 29(20), С. R1094 - R1103

Опубликована: Окт. 1, 2019

Язык: Английский

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

Trends in Genetics, Год журнала: 2019, Номер 36(2), С. 132 - 145

Опубликована: Дек. 24, 2019

Язык: Английский

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

Genome biology, Год журнала: 2020, Номер 21(1)

Опубликована: Ноя. 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.

Язык: Английский

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

Nature Genetics, Год журнала: 2023, Номер 55(8), С. 1390 - 1399

Опубликована: Июль 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.

Язык: Английский

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

BMC Biology, Год журнала: 2020, Номер 18(1)

Опубликована: Фев. 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.

Язык: Английский

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Fungal evolution: cellular, genomic and metabolic complexity

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Год журнала: 2020, Номер 95(5), С. 1198 - 1232

Опубликована: Апрель 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.

Язык: Английский

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

Nature Microbiology, Год журнала: 2021, Номер 6(12), С. 1526 - 1536

Опубликована: Ноя. 24, 2021

Язык: Английский

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

Microbiome, Год журнала: 2021, Номер 9(1)

Опубликована: Март 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.

Язык: 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, Год журнала: 2021, Номер 233(3), С. 1097 - 1107

Опубликована: Ноя. 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.

Язык: Английский

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The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high levels of lineage-specific diversity driven by recombination

PLoS Biology, Год журнала: 2022, Номер 20(11), С. e3001890 - e3001890

Опубликована: Ноя. 17, 2022

Aspergillus fumigatus is a deadly agent of human fungal disease where virulence heterogeneity thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail capture intraspecific in genes absent from the genome. Pan-genomic de novo assemblies promising alternative reference-based genomics with potential address full repertoire species. Here, we evaluate 260 sequences A . including 62 newly sequenced strains, using combination genomics, phylogenomics, and pan-genomics. Our results high-resolution assessment structure recombination frequency, phylogenetically presence–absence variation, evidence for metabolic specificity, distribution putative antifungal resistance genes. Although disperses primarily via asexual conidia, identified extraordinarily high levels lowest linkage disequilibrium decay value reported any species date. We provide 3 primary populations , occurring only rarely often within them. These both distinct patterns unique suites accessory present exclusively each clade. Accessory displayed functional enrichment nitrogen carbohydrate metabolism suggesting that may stratified environmental niche specialization. Similarly, alleles were phylogeny. Altogether, pan-genome represents one largest pan-genomes date many unrepresented Af293 highlight inadequacy relying single-reference genome-based approach evaluating power combined elucidate structure, diversity, ecological drivers clinically relevant fungi.

Язык: Английский

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