Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing

Genome biology, Journal Year: 2022, Volume and Issue: 23(1)

Published: Dec. 15, 2022

Advancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for automating assembly scaffolding and patching, establish chromosome-scale reference genomes the widely used tomato genotype M82 along with Sweet-100, new rapid-cycling that developed to accelerate functional editing in tomato. This work outlines strategies rapidly expand genomic resources other plant species.

Language: Английский

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quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

Horticulture Research, Journal Year: 2023, Volume and Issue: 10(8)

Published: June 13, 2023

A high-quality genome is the basis for studies on functional, evolutionary, and comparative genomics. The majority of attention has been paid to solution complex chromosome structures highly repetitive sequences, along with emergence a new 'telomere-to-telomere (T2T) assembly' era. However, bioinformatic tools automatic construction and/or characterization T2T are limited. Here, we developed user-friendly web toolkit, quarTeT, which currently includes four modules: AssemblyMapper, GapFiller, TeloExplorer, CentroMiner. First, AssemblyMapper designed assemble phased contigs into chromosome-level by referring closely related genome. Then, GapFiller would endeavor fill all unclosed gaps in given aid additional ultra-long sequences. Finally, TeloExplorer CentroMiner applied identify candidate telomere centromere as well their localizations each chromosome. These modules can be used alone or combination other assembly characterization. As case study, adopting entire modular functions have achieved

Language: Английский

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The giant diploid faba genome unlocks variation in a global protein crop

Nature, Journal Year: 2023, Volume and Issue: 615(7953), P. 652 - 659

Published: March 8, 2023

Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss biodiversity1. However, production is hampered by lack a cool-season legume equivalent to soybean agronomic value2. Faba bean (Vicia faba L.) has high yield potential well suited for cultivation temperate regions, but genomic resources are scarce. Here, we report high-quality chromosome-scale assembly genome show that it expanded massive 13 Gb size through an imbalance between rates amplification elimination retrotransposons satellite repeats. Genes recombination events evenly dispersed across chromosomes gene space remarkably compact considering size, although with substantial copy number variation driven tandem duplication. Demonstrating practical application sequence, develop targeted genotyping assay use high-resolution genome-wide association analysis dissect genetic basis seed hilum colour. The presented constitute genomics-based breeding platform bean, enabling breeders geneticists accelerate improvement sustainable Mediterranean, subtropical northern agroecological zones.

Language: Английский

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Cycles of satellite and transposon evolution in Arabidopsis centromeres

Nature, Journal Year: 2023, Volume and Issue: 618(7965), P. 557 - 565

Published: May 17, 2023

Language: Английский

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JCVI: A versatile toolkit for comparative genomics analysis

iMeta, Journal Year: 2024, Volume and Issue: 3(4)

Published: June 12, 2024

Abstract The life cycle of genome builds spans interlocking pillars assembly, annotation, and comparative genomics to drive biological insights. While tools exist address each pillar separately, there is a growing need for integrate different project holistically. For example, approaches can provide quality control assembly or annotation; in turn, help identify artifacts that may complicate the interpretation comparisons. JCVI library versatile Python‐based offers suite excel across these pillars. Featuring modular design, provides high‐level utilities tasks such as format parsing, graphics generation, manipulation assemblies annotations. Supporting algorithms like MCscan ALLMAPS are widely employed building releases, producing publication‐ready figures assessment evolutionary inference. Developed maintained collaboratively, emphasizes reusability.

Language: Английский

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HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Jan. 28, 2023

Abstract The complex and dynamic three-dimensional organization of chromatin within the nucleus makes understanding control gene expression challenging, but also opens up possible ways to epigenetically modulate expression. Because plants are sessile, they evolved sophisticated rapidly in response environmental stress, that thought be coordinated by changes conformation mediate specific cellular physiological responses. However, what extent how stress induces reorganization remains poorly understood. Here, we comprehensively investigated genome-wide associated with transcriptional reprogramming heat tomato. Our data show rapid architecture, leading transient formation promoter-enhancer contacts, likely driving heat-stress responsive genes. Furthermore, demonstrate spatial requires HSFA1a, a transcription factor (TF) essential for tolerance In light our findings, propose TFs play key role controlling responses through 3D reconfiguration contacts.

Language: Английский

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The pan-genome and local adaptation of Arabidopsis thaliana

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Oct. 6, 2023

Abstract Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution genomic structural variations (SVs) and their associate genes to local adaptation this widely distribute remains unclear. Here, we de novo assemble chromosome-level genomes 32 A. ecotypes determine that variable expand gene pool in different thus assist adaptation. We develop graph-based pan-genome identify 61,332 SVs overlap with 18,883 genes, some which are highly involved ecological species. For instance, observe specific 332 bp insertion promoter region HPCA1 Tibet-0 ecotype enhances expression, thereby promotes alpine environments. These findings augment our understanding molecular mechanisms underlying across diverse habitats.

Language: Английский

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Convergent evolution of plant prickles by repeated gene co-option over deep time

Science, Journal Year: 2024, Volume and Issue: 385(6708)

Published: Aug. 1, 2024

An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses prickles-sharp epidermal projections-that convergently evolved numerous plant lineages. Mutations a cytokinin hormone biosynthetic gene caused at least 16 independent prickles eggplants wild relatives genus

Language: Английский

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Population comparative genomics discovers gene gain and loss during grapevine domestication

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(2), P. 1401 - 1413

Published: Jan. 29, 2024

Abstract Plant domestication are evolutionary experiments conducted by early farmers since thousands years ago, during which the crop wild progenitors artificially selected for desired agronomic traits along with dramatic genomic variation in course of moderate to severe bottlenecks. However, previous investigations mainly focused on small-effect variants, while changes gene contents rarely investigated due lack population-level assemblies both and its relatives. Here, we applied comparative analyses discover gain loss grapevine using long-read representative population samples domesticated grapevines (V. vinifera ssp. vinifera) their sylvestris). Only ∼7% families were shared 16 Vitis genomes ∼8% specific each accession, suggesting variations genomes. Compared progenitors, accessions exhibited an increased presence genes associated asexual reproduction, showcased a higher abundance related pollination, revealing transition from sexual reproduction clonal propagation processes. Moreover, harbored fewer disease-resistance than progenitors. The SVs occurred frequently aroma between indicating rapid diversification these domestication. Our study provides insights resources biological studies breeding programs grapevine.

Language: Английский

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Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories

Science, Journal Year: 2025, Volume and Issue: 387(6729)

Published: Jan. 2, 2025

Balanced mating type polymorphisms offer a distinct window into the forces shaping sexual reproduction strategies. Multiple hermaphroditic genera in Juglandaceae, including walnuts ( Juglans ) and hickories Carya ), show 1:1 genetic dimorphism for male versus female flowering order (heterodichogamy). We map two Mendelian inheritance mechanisms to ancient (>37 million years old) genus-wide structural DNA polymorphisms. The dominant haplotype female-first contains tandem repeats of 3′ untranslated region gene putatively involved trehalose-6-phosphate metabolism is associated with increased cis expression developing flowers, possibly mediated by small RNAs. locus ~20 syntenic genes shows molecular signatures sex chromosome–like evolution. Inheritance heterodichogamy are deeply conserved, yet may occasionally turn over, as determination.

Language: Английский

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