Phased telomere-to-telomere reference genome and pangenome reveal an expansion of resistance genes during apple domestication

PLANT PHYSIOLOGY, Год журнала: 2024, Номер 195(4), С. 2799 - 2814

Опубликована: Май 14, 2024

Abstract The cultivated apple (Malus domestica Borkh.) is a cross-pollinated perennial fruit tree of great economic importance. Earlier versions reference genomes were unphased, fragmented, and lacked comprehensive insights into the apple's highly heterozygous genome, which impeded advances in genetic studies breeding programs. In this study, we assembled haplotype-resolved telomere-to-telomere (T2T) genome for diploid cultivar Golden Delicious. Subsequently, constructed pangenome based on 12 assemblies from wild species to investigate dynamic changes functional genes. Our results revealed gene gain loss events during domestication. Compared with species, more families significantly enriched oxidative phosphorylation, pentose metabolic process, responses salt, abscisic acid biosynthesis process. analyses also demonstrated higher prevalence different types resistance analogs (RGAs) cultivars than their relatives, partially attributed segmental tandem duplication certain RGAs classes. Structural variations, mainly deletions insertions, have affected presence absence TIR-NB-ARC-LRR, NB-ARC-LRR, CC-NB-ARC-LRR Additionally, hybridization/introgression has contributed expansion genes domesticated apples. T2T provide important resources apples, emphasizing need study evolutionary mechanisms breeding.

Язык: Английский

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Genome resources for three modern cotton lines guide future breeding efforts

Nature Plants, Год журнала: 2024, Номер 10(6), С. 1039 - 1051

Опубликована: Май 30, 2024

Abstract Cotton ( Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and quality show high variability due to genotype-specific traits complex interactions among cultivars, management practices environmental factors. Modern breeding may limit future gains a narrow founding gene pool. Precision biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars (‘UGA230’, ‘UA48’ ‘CSX8308’) updating ‘TM-1’ genetic standard reference. Despite hypothesized uniformity, considerable sequence structural variation was observed four genomes, which overlap with ancient ongoing genomic introgressions from ‘Pima’ cotton, regulatory mechanisms phenotypic trait divergence. Differentially expressed genes across development correlate production, potentially contributing distinctive in cultivars. These comparative analyses provide valuable foundation endeavours enhance global sustainability.

Язык: Английский

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Chromosome-level genome assemblies reveal genome evolution of an invasive plant Phragmites australis

Communications Biology, Год журнала: 2024, Номер 7(1)

Опубликована: Авг. 17, 2024

Biological invasions pose a significant threat to ecosystems, disrupting local biodiversity and ecosystem functions. The genomic underpinnings of invasiveness, however, are still largely unknown, making it difficult predict manage invasive species effectively. common reed (Phragmites australis) is dominant grass in wetland ecosystems has become particularly when transferred from Europe North America. Here, we present high-quality gap-free, telomere-to-telomere genome assembly Phragmites australis consisting 24 pseudochromosomes B chromosome. Fully phased subgenomes demonstrated considerable subgenome dominance revealed the divergence diploid progenitors approximately 30.9 million years ago. Comparative genomics using chromosome-level scaffolds for three other lineages previously published draft an lineage that gene family expansions form tandem duplications may have contributed invasiveness lineage. This study sheds light on evolution Arundinoideae grasses suggests genetic drivers, such as duplications, underly processes biological invasion plants. These findings provide crucial step toward understanding managing basis plant species.

Язык: Английский

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Chromosome-level analysis of the Colletotrichum graminicola genome reveals the unique characteristics of core and minichromosomes

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Март 23, 2023

The fungal pathogen

Язык: Английский

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Haplotype‐resolved genome assembly of Populus tremula × P. alba reveals aspen‐specific megabase satellite DNA

The Plant Journal, Год журнала: 2023, Номер 116(4), С. 1003 - 1017

Опубликована: Сен. 7, 2023

Populus species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy bioproducts. Hybrid aspen tremula × P. alba INRA 717-1B4 is widely used transformation model tree functional genomics biotechnology research. As an outcrossing interspecific hybrid, its genome riddled with sequence polymorphisms which present challenge sequence-sensitive analyses. Here we report telomere-to-telomere this hybrid two chromosome-scale, haplotype-resolved assemblies. We performed comprehensive analysis of the repetitive landscape identified both tandem repeat array-based array-less centromeres. Unexpectedly, most abundant satellite repeats haplotypes lie outside centromeres, consist 147 bp monomer PtaM147, frequently span >1 megabases, form heterochromatic knobs. PtaM147 detected exclusively aspens (section Populus) but PtaM147-like sequences occur LTR-retrotransposons closely related species, suggesting their origin from retrotransposons. The genomic resource generated genotype has greatly improved design editing experiments that highly sensitive to polymorphisms. work should motivate future hypothesis-driven research probe into function aspen-specific DNA.

Язык: Английский

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