Genome evolution and diversity of wild and cultivated potatoes

Nature, Год журнала: 2022, Номер 606(7914), С. 535 - 541

Опубликована: Июнь 8, 2022

Potato (Solanum tuberosum L.) is the world's most important non-cereal food crop, and vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have potential to revolutionize future potato production1-4. So far, relatively few studies examined genome evolution diversity wild cultivated landrace potatoes, which limits application their breeding. Here we assemble 44 high-quality genomes from 24 20 accessions that representative Solanum section Petota, tuber-bearing clade, as well 2 neighbouring section, Etuberosum. Extensive discordance phylogenomic relationships suggests complexity evolution. We find substantially expanded its repertoire disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative effect tuber-based propagation strategies genome. discover a transcription factor determines tuber identity interacts mobile tuberization inductive signal SP6A. also identify 561,433 high-confidence structural variants construct map large inversions, provides insights for improving inbred lines precluding linkage drag, exemplified by 5.8-Mb inversion associated carotenoid content tubers. This study will accelerate enrich our understanding biology global staple crop.

Язык: Английский

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A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors

Cell, Год журнала: 2022, Номер 185(20), С. 3807 - 3822.e12

Опубликована: Сен. 1, 2022

Язык: Английский

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FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data

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

Опубликована: Дек. 1, 2020

Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools often single-purpose, or limited in compatibility a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we present FAN-C, an easy-to-use command-line tool powerful Python API with broad feature set covering matrix generation, analysis, visualisation for C-like ( https://github.com/vaquerizaslab/fanc ). Due its the most prevalent storage FAN-C can be used combination large existing tools, thus greatly simplifying analysis.

Язык: Английский

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A genome-scale screen for synthetic drivers of T cell proliferation

Nature, Год журнала: 2022, Номер 603(7902), С. 728 - 735

Опубликована: Март 16, 2022

Язык: Английский

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Repeat-based holocentromeres influence genome architecture and karyotype evolution

Cell, Год журнала: 2022, Номер 185(17), С. 3153 - 3168.e18

Опубликована: Авг. 1, 2022

The centromere represents a single region in most eukaryotic chromosomes. However, several plant and animal lineages assemble holocentromeres along the entire chromosome length. Here, we compare genome organization evolution as function of type by assembling chromosome-scale holocentric genomes with repeat-based from three beak-sedge (Rhynchospora pubera, R. breviuscula, tenuis) their closest monocentric relative, Juncus effusus. We demonstrate that transition to holocentricity affected 3D architecture redefining genomic compartments, while distributing thousands units genome-wide. uncover complex pubera hides its unexpected octoploidy describe marked reduction number for tenuis, which has only two show fusions, facilitated holocentromeres, promoted karyotype diploidization. Our study thus sheds light on important aspects influenced organization.

Язык: Английский

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RNA polymerase II dynamics shape enhancer–promoter interactions

Nature Genetics, Год журнала: 2023, Номер 55(8), С. 1370 - 1380

Опубликована: Июль 10, 2023

Язык: Английский

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Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin

Science, Год журнала: 2023, Номер 381(6653), С. 92 - 100

Опубликована: Июль 6, 2023

Nanoscale chromatin organization regulates gene expression. Although is notably reprogrammed during zygotic genome activation (ZGA), the of regulatory factors this universal process remains unclear. In work, we developed expansion microscopy (ChromExM) to visualize chromatin, transcription, and transcription in vivo. ChromExM embryos ZGA revealed how pioneer factor Nanog interacts with nucleosomes RNA polymerase II (Pol II), providing direct visualization transcriptional elongation as string-like nanostructures. Blocking led more Pol particles clustered around Nanog, stalled at promoters Nanog-bound enhancers. This a new model termed "kiss kick", which enhancer-promoter contacts are transient released by elongation. Our results demonstrate that broadly applicable study nanoscale nuclear organization.

Язык: Английский

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Annelid functional genomics reveal the origins of bilaterian life cycles

Nature, Год журнала: 2023, Номер 615(7950), С. 105 - 110

Опубликована: Янв. 25, 2023

Язык: Английский

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Single-nucleus RNA-sequencing of autosomal dominant Alzheimer disease and risk variant carriers

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Апрель 21, 2023

Genetic studies of Alzheimer disease (AD) have prioritized variants in genes related to the amyloid cascade, lipid metabolism, and neuroimmune modulation. However, cell-specific effect these is not fully understood. Here, we perform single-nucleus RNA-sequencing (snRNA-seq) on nearly 300,000 nuclei from parietal cortex AD autosomal dominant (APP PSEN1) risk-modifying variant (APOE, TREM2 MS4A) carriers. Within individual cell types, capture commonly dysregulated across groups. specific transcriptional states are more prevalent within oligodendrocytes show a autophagy-lysosomal pathway, MS4A microglia complement cascade genes, APOEε4 inhibitory neurons display signs ferroptosis. All types enriched We leverage differential expression ATAC-seq map GWAS signals effector including NCK2 signal addition initially proposed microglia. Overall, our results provide insights into diversity resulting genetic architecture cellular heterogeneity. The data can be explored online browser ( http://web.hararilab.org/SNARE/ ).

Язык: Английский

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CRISPR screens decode cancer cell pathways that trigger γδ T cell detection

Nature, Год журнала: 2023, Номер 621(7977), С. 188 - 195

Опубликована: Авг. 30, 2023

Язык: Английский

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