Multiple wheat genomes reveal global variation in modern breeding

Nature, Journal Year: 2020, Volume and Issue: 588(7837), P. 277 - 283

Published: Nov. 25, 2020

Abstract Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts wheat ( Triticum spp.) been more challenging. This is largely owing to size and complexity genome 1 , lack genome-assembly data for multiple lines 2,3 . Here we generated ten chromosome pseudomolecule five scaffold assemblies hexaploid explore genomic diversity among from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions wild relatives differences gene content resulting complex histories aimed at improving adaptation diverse environments, grain yield quality, resistance stresses 4,5 We provide examples outlining utility these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved disease characterization Sm1 6 associated with insect resistance. These will basis functional discovery deliver next generation modern cultivars.

Language: Английский

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Durum wheat genome highlights past domestication signatures and future improvement targets

Nature Genetics, Journal Year: 2019, Volume and Issue: 51(5), P. 885 - 895

Published: April 8, 2019

The domestication of wild emmer wheat led to the selection modern durum wheat, grown mainly for pasta production. We describe 10.45 gigabase (Gb) assembly genome cultivar Svevo. enabled genome-wide genetic diversity analyses revealing changes imposed by thousands years empirical and breeding. Regions exhibiting strong signatures divergence associated with breeding were widespread in several major losses pericentromeric regions. A locus on chromosome 5B carries a gene encoding metal transporter (TdHMA3-B1) non-functional variant causing high accumulation cadmium grain. high-cadmium allele, among cultivars but undetected accessions, increased frequency from domesticated wheat. rapid cloning TdHMA3-B1 rescues beneficial allele demonstrates practical use Svevo improvement. Genome enables highlighting modifications

Language: Английский

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The Dfam community resource of transposable element families, sequence models, and genome annotations

Mobile DNA, Journal Year: 2021, Volume and Issue: 12(1)

Published: Jan. 12, 2021

Abstract Dfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0–3.3 releases ( https://dfam.org ) represent evolution from a proof-of-principle collection transposable element families in model organisms into community resource for broad range species, both curated uncurated datasets. In addition, since 3.0 provide auxiliary consensus protein alignments, formalized classification system to support the growing diversity represented resource. latest release includes 266,740 new de novo generated 336 species contributed by EBI. This expansion demonstrates utility many Dfam’s features provides insight long term challenges ahead improving

Language: Английский

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pyGenomeTracks: reproducible plots for multivariate genomic datasets

Bioinformatics, Journal Year: 2020, Volume and Issue: 37(3), P. 422 - 423

Published: July 27, 2020

Abstract Motivation Generating publication ready plots to display multiple genomic tracks can pose a serious challenge. Making desirable and accurate figures requires considerable effort. This is usually done by hand or using vector graphic software. Results pyGenomeTracks (PGT) modular plotting tool that easily combines tracks. It enables reproducible standardized generation of highly customizable images. Availability implementation PGT available through graphical interface on https://usegalaxy.eu the command line. provided conda via bioconda channel, pip it openly developed github: https://github.com/deeptools/pyGenomeTracks. Supplementary information data are at Bioinformatics online.

Language: Английский

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Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly

The Plant Journal, Journal Year: 2021, Volume and Issue: 107(1), P. 303 - 314

Published: April 24, 2021

Summary Until recently, achieving a reference‐quality genome sequence for bread wheat was long thought beyond the limits of sequencing and assembly technology, primarily due to large size > 80% repetitive content. The release chromosome scale 14.5‐Gb IWGSC RefSeq v1.0 cv. Chinese Spring (CS) was, therefore, milestone. Here, we used direct label stain (DLS) optical map CS together with prior nick, label, repair (NLRS) map, contigs assembled Pacific Biosciences reads, refine assembly. Inconsistencies between maps were reconciled gaps closed. Gap filling anchoring 279 unplaced scaffolds increased total length pseudomolecules by 168 Mb (excluding Ns). Positions orientations corrected 233 354 scaffolds, respectively, representing 10% sequence. accuracy remaining 90% validated. As result contiguity, numbers transposable elements (TEs) intact TEs have in v2.1 compared v1.0. In total, 98% gene models identified mapped onto this new through development dedicated approach implemented MAGAAT pipeline. high‐confidence genes on from 105 319 534. enhances utility genetic mapping, comparative genomics, annotation isolation, more general studies biology wheat.

Language: Английский

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Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

Mobile DNA, Journal Year: 2019, Volume and Issue: 10(1)

Published: Jan. 3, 2019

Plant LTR-retrotransposons are classified into two superfamilies, Ty1/copia and Ty3/gypsy. They further divided an enormous number of families which are, due to the high diversity their nucleotide sequences, usually specific a single or group closely related species. Previous attempts these broader categories reflecting phylogenetic relationships were limited either analyzing narrow range plant species small numbers elements. Furthermore, there is no reference database that allows for similarity based classification LTR-retrotransposons.

Language: Английский

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RNA-directed DNA Methylation

PLoS Genetics, Journal Year: 2020, Volume and Issue: 16(10), P. e1009034 - e1009034

Published: Oct. 8, 2020

RNA-directed DNA methylation (RdDM) is a biological process in which non-coding RNA molecules direct the addition of to specific sequences. The RdDM pathway unique plants, although other mechanisms chromatin modification have also been described fungi and animals. To date, best characterized within angiosperms (flowering plants), particularly model plant Arabidopsis thaliana. However, conserved components associated small RNAs (sRNAs) found groups such as gymnosperms ferns. closely resembles sRNA pathways, highly RNAi fungi, Both pathways produce sRNAs involve Argonaute, Dicer RNA-dependent polymerase proteins. has implicated number regulatory processes plants. added by generally with transcriptional repression genetic sequences targeted pathway. Since patterns plants are heritable, these changes can often be stably transmitted progeny. As result, one prominent role stable, transgenerational suppression transposable element (TE) activity. linked pathogen defense, abiotic stress responses, regulation several key developmental transitions. Although important functions, RdDM-defective mutants thaliana viable reproduce, enabled detailed studies range defects different species, including lethality, altered reproductive phenotypes, TE upregulation genome instability, increased sensitivity. Overall, an that regulates establishing reinforcing patterns, lead epigenetic effects on gene expression phenotype.

Language: Английский

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A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes

Nature Genetics, Journal Year: 2021, Volume and Issue: 53(4), P. 574 - 584

Published: March 18, 2021

Abstract Rye is a valuable food and forage crop, an important genetic resource for wheat triticale improvement indispensable material efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted 98.47% estimated size (7.86 Gb), with 93.67% (7.25 assigned to seven chromosomes. Repetitive elements constituted 90.31% genome. Compared previously Triticeae genomes, Daniela , Sumaya Sumana retrotransposons showed strong expansion rye. Further analyses assembly shed new light on genome-wide gene duplications their impact starch biosynthesis genes, physical organization complex prolamin loci, expression features underlying early heading trait putative domestication-associated chromosomal regions loci This sequence promises accelerate breeding related cereal crops.

Language: Английский

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Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

Nature Genetics, Journal Year: 2021, Volume and Issue: 53(4), P. 564 - 573

Published: March 18, 2021

Abstract Rye ( Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary enable hybrid breeding. allogamous only recently domesticated, thus giving cultivated ryes access a diverse exploitable wild gene pool. To further enhance agronomic potential rye, we produced chromosome-scale annotated assembly 7.9-gigabase rye genome validated its quality by using suite molecular genetic resources. We demonstrate applications this resource with broad range investigations. present findings on rye’s incomplete isolation from relatives, mechanisms structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for breeding yield benefits rye–wheat introgressions.

Language: Английский

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Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat

Genome biology, Journal Year: 2019, Volume and Issue: 20(1)

Published: July 12, 2019

Bread wheat is one of the most important and broadly studied crops. However, due to complexity its genome incomplete collection wild populations, bread landscape domestication history remain elusive.By investigating whole-genome resequencing data 93 accessions from worldwide populations diploid tetraploid progenitors, together with 90 published exome-capture data, we find that B subgenome has more variations than A D subgenomes, including SNPs deletions. Population genetics analyses support a monophyletic origin domesticated emmer in northern Levant, substantial introgressed genomic fragments southern Levant. Southern Levant contributes 676 Mb AB subgenomes enriched pericentromeric regions. The introgression happens at early stage speciation partially their greater genetic diversity. Furthermore, detect massive alien introgressions originated distant species through natural artificial hybridizations, resulting reintroduction ~ 709 1577 sequences into landraces varieties, respectively. large fraction these intra- inter-introgression are associated quantitative trait loci traits, selection events also identified.We reveal significance multiple shaping components wheat, provide resources new perspectives for future breeding.

Language: Английский

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