WheatOmics: A platform combining multiple omics data to accelerate functional genomics studies in wheat

Molecular Plant, Год журнала: 2021, Номер 14(12), С. 1965 - 1968

Опубликована: Окт. 27, 2021

Язык: Английский

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Twenty years of plant genome sequencing: achievements and challenges

Trends in Plant Science, Год журнала: 2021, Номер 27(4), С. 391 - 401

Опубликована: Ноя. 12, 2021

Язык: Английский

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GENESPACE tracks regions of interest and gene copy number variation across multiple genomes

eLife, Год журнала: 2022, Номер 11

Опубликована: Сен. 9, 2022

The development of multiple chromosome-scale reference genome sequences in many taxonomic groups has yielded a high-resolution view the patterns and processes molecular evolution. Nonetheless, leveraging information across genomes remains significant challenge nearly all eukaryotic systems. These challenges range from studying evolution chromosome structure, to finding candidate genes for quantitative trait loci, testing hypotheses about speciation adaptation. Here, we present GENESPACE, which addresses these by integrating conserved gene order orthology define expected physical position genomes. We demonstrate this utility dissecting presence-absence, copy-number, structural variation at three levels biological organization: spanning 300 million years vertebrate sex evolution, diversity Poaceae (grass) plant family, among 26 maize cultivars. methods build visualize syntenic GENESPACE R package offer addition existing family synteny programs, especially polyploid, outbred, other complex genomes.The is complete DNA sequence an individual. It crucial foundation studies medicine, agriculture, conservation biology. Advances genetics have made it possible rapidly sequence, or read out, organisms. For closely related species, scientists can then do detailed comparisons, revealing similar with shared past common role, but comparing more distantly organisms difficult. One major that are often lost duplicated over evolutionary time. way be confident look ‘synteny’, how organized ordered within genome. In some persists millions Combining similarity could make comparisons between species robust. To this, Lovell et al. developed software links similarities This allows researchers explore determine whether been duplicated. value explored vertebrates flowering plants. was able highlight unique chromosomes birds mammals, track positions important grass crops including maize, wheat, rice. Exploring genetic code lead better understanding sections might also allow find target applications like crop improvement. designed easy use, allowing them graphics perform analyses few programming skills.

Язык: Английский

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Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning

Nature Genetics, Год журнала: 2022, Номер 54(3), С. 227 - 231

Опубликована: Март 1, 2022

Abstract The cloning of agronomically important genes from large, complex crop genomes remains challenging. Here we generate a 14.7 gigabase chromosome-scale assembly the South African bread wheat ( Triticum aestivum ) cultivar Kariega by combining high-fidelity long reads, optical mapping and chromosome conformation capture. resulting is an order magnitude more contiguous than previous assemblies. shows durable resistance to devastating fungal stripe rust disease 1 . We identified race-specific gene Yr27 , which encodes intracellular immune receptor, be major contributor this resistance. allelic leaf Lr13 ; proteins show 97% sequence identity 2,3 Our results demonstrate feasibility generating assemblies clone genes, exemplify that highly similar alleles single-copy can confer different pathogens, might provide basis for engineering with multiple recognition specificities in future.

Язык: Английский

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Chromosome-scale genome assembly of the transformation-amenable common wheat cultivar ‘Fielder’

DNA Research, Год журнала: 2021, Номер 28(3)

Опубликована: Июнь 1, 2021

Abstract We have established a high-quality, chromosome-level genome assembly for the hexaploid common wheat cultivar ‘Fielder’, an American, soft, white, pastry-type released in 1974 and known its amenability to Agrobacterium tumefaciens-mediated transformation editing. Accurate, long-read sequences were obtained using PacBio circular consensus sequencing with HiFi approach. Sequence reads from 16 SMRT cells assembled hifiasm assembler produced assemblies N50 greater than 20 Mb. used Omni-C chromosome conformation capture technique order contigs into assemblies, resulting 21 pseudomolecules cumulative size of 14.7 0.3 Gb unanchored contigs. Mapping published short transgenic plant edited seed-dormancy gene, TaQsd1, identified four positions transgene insertion chromosomes. Detection guide RNA provided candidates off-target mutation induction. These results demonstrate efficiency chromosome-scale their application genome-editing studies.

Язык: Английский

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TaCol-B5 modifies spike architecture and enhances grain yield in wheat

Science, Год журнала: 2022, Номер 376(6589), С. 180 - 183

Опубликована: Апрель 7, 2022

Spike architecture influences grain yield in wheat. We report the map-based cloning of a gene determining number spikelet nodes per spike common The cloned is named TaCOL-B5 and encodes CONSTANS-like protein that orthologous to COL5 plant species. Constitutive overexpression dominant TaCol-B5 allele but without region encoding B-boxes wheat cultivar increases produces more tillers spikes, thereby enhancing transgenic plants under field conditions. Allelic variation results amino acid substitutions leading differential phosphorylation by kinase TaK4. present emmer rare global collection modern cultivars.

Язык: Английский

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An unusual tandem kinase fusion protein confers leaf rust resistance in wheat

Nature Genetics, Год журнала: 2023, Номер 55(6), С. 914 - 920

Опубликована: Май 22, 2023

The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with disease-resistance genes1. Here we use mutagenesis and transcriptome sequencing clone the leaf rust resistance gene Lr9, which was introduced into bread wheat grass species Aegilops umbellulata2. We that Lr9 encodes unusual tandem kinase fusion protein. Long-read a line putative Ae. umbellulata donor enabled us assemble ~28.4-Mb translocation identify breakpoint. likewise cloned Lr58, reportedly introgressed triuncialis3, but has identical coding sequence compared Lr9. Cytogenetic haplotype analyses corroborate two genes originate same event. Our work sheds light on emerging role proteins in disease resistance, expanding repertoire for breeding.

Язык: Английский

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Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Plant Communications, Год журнала: 2023, Номер 5(1), С. 100646 - 100646

Опубликована: Июль 6, 2023

Gene cloning in repeat-rich polyploid genomes remains challenging. Here we describe a strategy for overcoming major bottlenecks the of powdery mildew (Pm) resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat (WEW). A conventional positional approach was not effective due to suppressed recombination. Chromosome sorting compromised by insufficient purity. physical map, constructed assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. single candidate NLR identified anchoring RNASeq reads susceptible mutants ONT contigs and validated virus-induced silencing. is likely newly evolved NLR, which discovered only one location across WEW distribution range Israel. successfully introgressed into cultivated wheat, diagnostic molecular marker used accelerate its deployment pyramiding other R-genes.

Язык: Английский

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shinyCircos‐V2.0: Leveraging the creation of Circos plot with enhanced usability and advanced features

iMeta, Год журнала: 2023, Номер 2(2)

Опубликована: Май 1, 2023

We previously developed shinyCircos, an interactive web application for creating Circos diagrams, which has been widely recognized its graphical user interface and ease of use. Here, we introduce shinyCircos-V2.0, upgraded version shinyCircos that includes a new with enhanced usability many features advanced plots. To help users get started provide detailed tutorials example input data sets. The is available online at https://venyao.xyz/shinyCircos/ https://asiawang.shinyapps.io/shinyCircos/, or can be installed locally using the source code deposited in GitHub (https://github.com/YaoLab-Bioinfo/shinyCircos-V2.0).

Язык: Английский

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Pm57 from Aegilops searsii encodes a tandem kinase protein and confers wheat powdery mildew resistance

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июнь 5, 2024

Abstract Powdery mildew is a devastating disease that affects wheat yield and quality. Wheat wild relatives represent valuable sources of resistance genes. Cloning characterization these genes will facilitate their incorporation into breeding programs. Here, we report the cloning Pm57 , powdery gene from Aegilops searsii . It encodes tandem kinase protein with putative kinase-pseudokinase domains followed by von Willebrand factor A domain (WTK-vWA), being ortholog Lr9 mediates leaf rust resistance. The function validated via independent mutants, silencing, transgenic assays. Stable lines introgression exhibit high levels all-stage to diverse isolates Bgt fungus, no negative impacts on agronomic parameters are observed in our experimental set-up. Our findings highlight emerging role fusion proteins plant provide for breeding.

Язык: Английский

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