Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Feb. 23, 2021

Sweet corn is one of the most important vegetables in United States and Canada. Here, we present a de novo assembly sweet inbred line Ia453 with mutated shrunken2-reference allele (Ia453-sh2). This mutation accumulates more sugar commercial hybrids developed for processing fresh markets. The ten pseudochromosomes cover 92% total 99% estimated genome size, scaffold N50 222.2 Mb. reference completely assembles large structural variation that created mutant sh2-R allele. Furthermore, comparative genomics analysis six field genomes highlights differences single-nucleotide polymorphisms, variations, transposon composition. Phylogenetic 5,381 diverse maize teosinte accessions reveals genetic relationships between other types maize. Our results show evidence common origin northern Mexico modern U.S. Finally, population genomic identifies regions under selection candidate genes associated traits, such as early flowering, endosperm composition, plant tassel architecture, kernel row number. study provides high-quality reference-genome sequence to facilitate genomics, functional studies, genomic-assisted breeding corn.

Language: Английский

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The pangenome of the wheat pathogen Pyrenophora tritici-repentis reveals novel transposons associated with necrotrophic effectors ToxA and ToxB

BMC Biology, Journal Year: 2022, Volume and Issue: 20(1)

Published: Oct. 24, 2022

In fungal plant pathogens, genome rearrangements followed by selection pressure for adaptive traits have facilitated the co-evolutionary arms race between hosts and their pathogens. Pyrenophora tritici-repentis (Ptr) has emerged recently as a foliar pathogen of wheat worldwide its populations consist isolates that vary in ability to produce combinations different necrotrophic effectors. These effectors play vital roles disease development. Here, we sequenced genomes global collection (40 isolates) Ptr gain insights into gene content rearrangements.A comparative analysis revealed an open pangenome, with abundance accessory genes (~ 57%) reflecting Ptr's adaptability. A clear distinction pathogenic non-pathogenic was observed size, content, phylogenetic relatedness. Chromosomal structural organization, specifically around effector coding genes, were detailed using long-read assemblies (PacBio RS II) generated this work addition previously assembled genomes. We also discovered involvement large mobile elements associated effectors: ToxA, encoding necrosis effector, found single copy within 143-kb 'Starship' transposon (dubbed 'Horizon') clearly defined target site duplications. 'Horizon' located on chromosomes isolates, indicating mobility, described ToxhAT (responsible horizontal transfer ToxA) nested newly identified Starship. Additionally, ToxB, chlorosis clustered three copies 294-kb element, which is likely putative 'Icarus') ToxB-producing isolate. ToxB missing from non-coding reference isolate, but homolog toxb 'Icarus' both present This suggests may been at some point during evolution contradictory current assumption vertical inheritance. Finally, architecture 'one-compartment' based calculated distances evolutionary rates.These findings together reflect highly plastic nature helped drive adaptation illuminated giant transposons facilitating virulence Ptr.

Language: Английский

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Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(2)

Published: Feb. 1, 2022

Abstract Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite importance supergenes in adaptation, little is known on how they originate. A classic example supergene S locus controlling heterostyly, a floral heteromorphism occurring 28 angiosperm families. In Primula, heterostyly characterized by cooccurrence two complementary, self-incompatible morphs and controlled five genes clustered hemizygous, ca. 300-kb locus. Here, we present first chromosome-scale genome assembly any heterostylous species, that Primula veris (cowslip). By leveraging high contiguity P. comparative analyses, demonstrated S-locus evolved via asynchronous gene duplications independent translocations. Furthermore, discovered new whole-genome duplication Ericales specific to lineage. We also propose mechanism for origin hemizygosity nonhomologous recombination involving newly pairs CFB flanking Finally, detected only weak signatures degeneration locus, as predicted hemizygous supergenes. The study provides useful resource future research addressing key questions evolution general particular: How do arise? What role architecture complex adaptations? Is molecular across angiosperms similar Primula?

Language: Английский

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Recurrent neo-sex chromosome evolution in kiwifruit

Nature Plants, Journal Year: 2023, Volume and Issue: 9(3), P. 393 - 402

Published: March 6, 2023

Language: Английский

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Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding

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

Published: April 17, 2023

Abstract Under-utilised orphan crops hold the key to diversified and climate-resilient food systems. Here, we report on crop genomics using case of Lablab purpureus (L.) Sweet (lablab) - a legume native Africa cultivated throughout tropics for forage. Our Africa-led plant genome collaboration produces high-quality chromosome-scale assembly lablab genome. highlights organisation trypsin inhibitor genes an important anti-nutritional factor in lablab. We also re-sequence wild accessions from confirming two domestication events. Finally, examine genetic phenotypic diversity comprehensive germplasm collection identify genomic loci underlying variation agronomic traits The data generated here provide valuable resource improvement. inclusive collaborative approach presents example that can be explored by other researchers sequencing indigenous crops, particularly low middle-income countries (LMIC).

Language: Английский

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Phased Assembly of Neo-Sex Chromosomes Reveals Extensive Y Degeneration and Rapid Genome Evolution in Rumex hastatulus

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(4)

Published: April 1, 2024

Abstract Y chromosomes are thought to undergo progressive degeneration due stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales evolutionary forces driving remain unclear. To investigate evolution sex on multiple timescales, we generated a high-quality phased genome assembly massive older (<10 MYA) neo (<200,000 yr) XYY cytotype dioecious plant Rumex hastatulus hermaphroditic outgroup salicifolius. Our assemblies, supported by fluorescence situ hybridization, confirmed that neo-sex were formed two key events: an X-autosome fusion reciprocal translocation between homologous autosome chromosome. The enormous sex-linked regions X (296 Mb) (503 both evolved from large repeat-rich genomic with low recombination; however, complete still led over 30% gene major rearrangements. In region, there has been significant increase transposable element abundance, even into near genes. neo-sex-linked regions, observed evidence extensive rearrangements without loss. Overall, inferred during first 10 million years chromosome but not very short timescales. results indicate when emerge repetitive already-low recombination, leads substantial content degeneration.

Language: Английский

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The genome awakens: transposon-mediated gene regulation

Trends in Plant Science, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

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The genome and GeneBank genomics of allotetraploid Nicotiana tabacum provide insights into genome evolution and complex trait regulation

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: March 26, 2025

Nicotiana tabacum is an allotetraploid hybrid of sylvestris and tomentosiformis a model organism in genetics. However, features subgenome evolution, expression coordination, genetic diversity complex traits regulation N. remain unresolved. Here we present chromosome-scale assemblies for all three species, genotype phenotypic data 5,196 germplasms. Chromosome rearrangements epigenetic modifications are associated with genome evolution coordination following polyploidization. Two subgenomes genes biased toward one contributed unevenly to trait variation. Using 178 marker–trait associations, reference genotype-to-phenotype map was built 39 morphological, developmental disease resistance traits, novel gene regulating leaf width validated. Signatures positive polygenic selection during the process selective breeding were detected. Our study provides insights into use GeneBank-scale resources advancing genomic research. Chromosome-level its ancestors, along their transcriptomes, epigenomes phenotype germplasms, provide regulation.

Language: Английский

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Measuring Performance Metrics of Machine Learning Algorithms for Detecting and Classifying Transposable Elements

Processes, Journal Year: 2020, Volume and Issue: 8(6), P. 638 - 638

Published: May 27, 2020

Because of the promising results obtained by machine learning (ML) approaches in several fields, every day is more common, utilization ML to solve problems bioinformatics. In genomics, a current issue detect and classify transposable elements (TEs) because tedious tasks involved bioinformatics methods. Thus, was recently evaluated for TE datasets, demonstrating better than applications. A crucial step selection metrics that measure realistic performance algorithms. Each metric has specific characteristics measures properties may be different from predicted results. Although most commonly used way compare using empirical analysis, non-result-based methodology been proposed, called invariance properties. These are calculated on basis whether given changes its value under certain modifications confusion matrix, giving comparative parameters independent datasets. Measure make or less informative, particularly unbalanced, monomodal, multimodal negative class datasets real simulated studies applied TEs, there no works evaluating tasks. Here, we analyzed 26 utilized binary, multiclass, hierarchical classifications, through bibliographic sources, their Then, corroborated our findings utilizing freely available Based suitable must stable, even highly unbalanced class, training with errors outliers. these parameters, conclude F1-score area precision-recall curve informative since they based other metrics, providing insight into development an application.

Language: Английский

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The sage genome provides insight into the evolutionary dynamics of diterpene biosynthesis gene cluster in plants

Cell Reports, Journal Year: 2022, Volume and Issue: 40(7), P. 111236 - 111236

Published: Aug. 1, 2022

Language: Английский

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