Genome sequences of four Ixodes species expands understanding of tick evolution

BMC Biology, Journal Year: 2025, Volume and Issue: 23(1)

Published: Jan. 21, 2025

Language: Английский

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The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 3, 2025

Language: Английский

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Structural polymorphism and diversity of human segmental duplications

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Abstract Segmental duplications (SDs) contribute significantly to human disease, evolution and diversity but have been difficult resolve at the sequence level. We present a population genetics survey of SDs by analyzing 170 genome assemblies (from 85 samples representing 38 Africans 47 non-Africans) in which majority autosomal are fully resolved using long-read assembly. Excluding acrocentric short arms sex chromosomes, we identify 173.2 Mb duplicated (47.4 not telomere-to-telomere reference) distinguishing fixed from structurally polymorphic events. find that intrachromosomal among most variable, with rare events mapping near their progenitor sequences. African genomes harbor more likely recently gene families higher copy numbers than non-African samples. Comparison resource 563 million full-length isoform sequencing reads identifies 201 novel, potentially protein-coding genes corresponding these number SDs.

Language: Английский

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Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Language: Английский

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The Marchantia polymorpha pangenome reveals ancient mechanisms of plant adaptation to the environment

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 17, 2025

Language: Английский

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Solanum pan-genetics reveals paralogues as contingencies in crop engineering

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

Published: March 5, 2025

Language: Английский

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Duckweed genomes and epigenomes underlie triploid hybridization and clonal reproduction

Current Biology, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

The Lemnaceae (duckweeds) are the world's smallest but fastest-growing flowering plants. Prolific clonal propagation facilitates continuous micro-cropping for plant-based protein and starch production holds tremendous promise sequestration of atmospheric CO2. Here, we present chromosomal assemblies, annotations, phylogenomic analysis Lemna genomes that uncover candidate genes responsible unique metabolic developmental traits family, such as anatomical reduction, adaxial stomata, lack stomatal closure, carbon via crystalline calcium oxalate. have selectively lost required RNA interference, including Argonaute reproductive isolation (the triploid block) haploid gamete formation. Triploid hybrids arise commonly among Lemna, found mutations in highly conserved meiotic crossover could support polyploid meiosis. Further, mapping centromeres by chromatin immunoprecipitation suggests their epigenetic origin despite divergence underlying tandem repeats centromeric retrotransposons. Syntenic comparisons with Wolffia Spirodela reveal diversification these genera coincided "Azolla event" mid-Eocene, during which aquatic macrophytes reduced high CO2 levels to those current ice age. Facile regeneration transgenic fronds from tissue culture, aided silencing, makes a powerful biotechnological platform, exemplified recent engineering high-oil outperforms oil-seed crops.

Language: 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, 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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Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: May 31, 2022

Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects sequence platform and assembly approach, or combining created by different approaches, on pangenome construction not investigated. Here we generate haplotype-resolved from the offspring three bovine trios representing increasing levels heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, accuracy current Bos taurus genome. Diploid coverage as low 20x HiFi 60x ONT is sufficient to produce two meeting standards set Vertebrate Genomes Project. Structural variant-based significant consensus regardless platform, assembler algorithm, coverage. Inspecting topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals affecting QRICH2, PRDM9, HSPA1A, TAS2R46, GC affect phenotype.

Language: Английский

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Gene mining and genomics-assisted breeding empowered by the pangenome of tea plant Camellia sinensis

Nature Plants, Journal Year: 2023, Volume and Issue: 9(12), P. 1986 - 1999

Published: Nov. 27, 2023

Language: Английский

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