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, Journal Year: 2022, Volume and Issue: 20(11), P. e3001890 - e3001890

Published: Nov. 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.

Language: Английский

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Recent advances in crustacean genomics and their potential application in aquaculture

Reviews in Aquaculture, Journal Year: 2023, Volume and Issue: 15(4), P. 1501 - 1521

Published: Jan. 23, 2023

Abstract Genomic resources are increasingly being used to improve the production efficiency and profitability of aquaculture. Crustaceans a large group invertebrates that encompasses some most important farmed species in aquaculture industry. However, very few crustacean genomes have been published although an genome project was proposed as early 1997. Breakthroughs next‐generation third‐generation sequencing technologies development high‐complexity sequence assembly strategies promoted publication increasing number genomes, thus paving broad way for biological genetic studies applications In this review, we summarize recent advances genomic research June 2022, including assembly, characteristics, mechanisms underlying various phenotypes, such environmental adaptation, lifestyle, development, sex determination. This review also discusses application aquaculture, dissection economic traits genome‐based selective breeding via genome‐wide association selection. High‐quality not only understanding basis biologically economically but improvement species. utilization genomics still lags far behind those other animals. Therefore, additional multi‐omics technological needed accelerate

Language: Английский

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Combined pangenomics and transcriptomics reveals core and redundant virulence processes in a rapidly evolving fungal plant pathogen

BMC Biology, Journal Year: 2023, Volume and Issue: 21(1)

Published: Feb. 6, 2023

Studying genomic variation in rapidly evolving pathogens potentially enables identification of genes supporting their "core biology", being present, functional and expressed by all strains or "flexible varying between strains. Genes flexible biology may be considered to "accessory", whilst the "core" gene set is likely important for common features a pathogen species biology, including virulence on host genotypes. The wheat-pathogenic fungus Zymoseptoria tritici represents one most threats global food security was focus this study.

Language: Английский

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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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FungANI, a BLAST-based program for analyzing average nucleotide identity (ANI) between two fungal genomes, enables easy fungal species delimitation

Fungal Genetics and Biology, Journal Year: 2025, Volume and Issue: 177, P. 103969 - 103969

Published: Jan. 31, 2025

Language: Английский

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Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 7, 2025

India harbors the world's largest cattle population, encompassing over 50 distinct Bos indicus breeds. This rich genetic diversity underscores inadequacy of a single reference genome to fully capture genomic landscape Indian cattle. To comprehensively characterize variation within and, specifically, dairy breeds, we aim identify non-reference sequences and construct comprehensive pangenome. Five representative genomes prominent including Gir, Kankrej, Tharparkar, Sahiwal, Red Sindhi, were sequenced using 10X Genomics 'linked-read' technology. Assemblies generated from these linked-reads ranged 2.70 Gb 2.77 Gb, comparable Brahman genome. A pangenome was constructed by comparing newly assembled with alignment graph-based methods, revealing 8 Mb 17.7 novel sequence respectively. confident set 6,844 Non-reference Unique Insertions (NUIs) spanning 7.57 identified through both representing Comparative analysis previously published pangenomes unveiled 2.8 (37%) commonality Chinese indicine only 1% taurus Among these, 2,312 NUIs ~ 2 Mb, commonly found in 98 samples 5 breeds designated as Common (BICIs) population. Furthermore, 926 BICIs 682 protein-coding genes, 54 long non-coding RNAs (lncRNA), 18 pseudogenes. These genes enriched for functions such chemical synaptic transmission, cell junction organization, cell-cell adhesion, morphogenesis. The various quantitative trait locus (QTL) regions, suggesting potential roles traits related milk production, reproduction, exterior, health, meat, carcass. Notably, 63.21% bases call contained interspersed repeats, predominantly Long Interspersed Nuclear Elements (LINEs). Additionally, 70.28% are shared other domesticated wild species, highlighting their evolutionary significance. is first report unveiling robust defining India. analyses contribute valuable insights into desi

Language: Английский

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The rise and fall of genes: origins and functions of plant pathogen pangenomes

Current Opinion in Plant Biology, Journal Year: 2020, Volume and Issue: 56, P. 65 - 73

Published: May 29, 2020

Plant pathogens can rapidly overcome resistance of their hosts by mutating key pathogenicity genes encoding for effectors. Pathogen adaptation is fuelled extensive genetic variability in populations and different strains may not share the same set genes. Recently, such an intra-specific variation gene content became formalized as pangenomes distinguishing core (i.e. shared) accessory lineage or strain-specific). Across species, effectors tend to be part evolving genome. Here, we show how construction analysis pathogen provide deep insights into dynamic host process. We also discuss should ideally built geography, niche lifestyle likely determine pangenome sizes.

Language: Английский

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Lateral Gene Transfer Mechanisms and Pan-genomes in Eukaryotes

Trends in Parasitology, Journal Year: 2020, Volume and Issue: 36(11), P. 927 - 941

Published: Aug. 19, 2020

Language: Английский

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Microevolution in the pansecondary metabolome of Aspergillus flavus and its potential macroevolutionary implications for filamentous fungi

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(21)

Published: May 20, 2021

Fungi produce a wealth of pharmacologically bioactive secondary metabolites (SMs) from biosynthetic gene clusters (BGCs). It is common practice for drug discovery efforts to treat species' metabolomes as being well represented by single or small number representative genomes. However, this approach misses the possibility that intraspecific population dynamics, such adaptation environmental conditions local microbiomes, may harbor novel BGCs contribute overall niche breadth species. Using 94 isolates Aspergillus flavus, cosmopolitan model fungus, sampled seven states in United States, we dereplicate 7,821 into 92 unique BGCs. We find more than 25% pangenomic show population-specific patterns presence/absence protein divergence. Population-specific make up most accessory-genome BGCs, suggesting different ecological forces maintain accessory genomes be partially mediated differences metabolism. use ultra-high-performance high-resolution mass spectrometry confirm these genetic also result chemotypic SM production populations, which could mediate interactions and acted on selection. Thus, our results suggest paradigm shift previously unrealized population-level reservoirs diversity significant evolutionary, ecological, pharmacological importance. Last, several A. flavus are present parasiticus minisclerotigenes discuss how microevolutionary uncover inform macroevolutionary inferences help align fungal metabolism with existing evolutionary theory.

Language: Английский

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A global phylogenomic analysis of the shiitake genus Lentinula

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(10)

Published: Feb. 27, 2023

Lentinula is a broadly distributed group of fungi that contains the cultivated shiitake mushroom, L. edodes . We sequenced 24 genomes representing eight described species and several unnamed lineages from 15 countries on four continents. comprises major clades arose in Oligocene, three Americas one Asia–Australasia. To expand sampling mushrooms, we assembled 60 China were previously published as raw Illumina reads added them to our dataset. sensu lato (s. lat.) may warrant recognition species, including single isolate Nepal sister rest s. lat., second with 20 cultivars 12 wild isolates China, Japan, Korea, Russian Far East, third 28 Thailand, Vietnam. Two additional have arisen by hybridization among groups. Genes encoding cysteine sulfoxide lyase ( lecsl ) γ-glutamyl transpeptidase leggt ), which are implicated biosynthesis organosulfur flavor compound lenthionine, diversified Paralogs both genes unique 3 5b) coordinately up-regulated fruiting bodies The pangenome lat. 20,308 groups orthologous genes, but only 6,438 orthogroups (32%) shared all strains, whereas 3,444 (17%) found populations, should be targeted for conservation.

Language: Английский

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