The Juicebox Assembly Tools module facilitatesde novoassembly of mammalian genomes with chromosome-length scaffolds for under $1000

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2018, Volume and Issue: unknown

Published: Jan. 28, 2018

Hi-C contact maps are valuable for genome assembly (Lieberman-Aiden, van Berkum et al. 2009; Burton 2013; Dudchenko 2017). Recently, we developed Juicebox, a system the visual exploration of data (Durand, Robinson 2016), and 3D-DNA, an automated pipeline using to assemble genomes (Dudchenko Here, introduce “Assembly Tools,” new module which provides point-and-click interface heatmaps identify correct errors in assembly. Together, 3D-DNA Juicebox Assembly Tools greatly reduce cost accurately assembling complex eukaryotic genomes. To illustrate, generated de novo assemblies with chromosome-length scaffolds three mammals: wombat, Vombatus ursinus (3.3Gb), Virginia opossum, Didelphis virginiana raccoon, Procyon lotor (2.5Gb). The only inputs each were Illumina reads from short insert DNA-Seq library (300 million reads, maximum length 2x150 bases) situ (100 read bases), <$1000.

Language: Английский

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Emerging and evolving concepts in gene essentiality

Nature Reviews Genetics, Journal Year: 2017, Volume and Issue: 19(1), P. 34 - 49

Published: Oct. 16, 2017

Language: Английский

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Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

Genome biology, Journal Year: 2018, Volume and Issue: 19(1)

Published: Aug. 14, 2018

The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access bread wheat reference genome sequence produced by International Wheat Genome Sequencing Consortium. browsers, BLAST, InterMine tools have established for in-depth exploration together additional linked datasets including physical maps, variations, gene expression, genetic phenomic data from other collaborative projects already stored in GnpIS information system. provides enhanced search browser features that will facilitate deployment latest genomics resources improvement.

Language: Английский

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Genome‐wide analysis of MIKC‐type MADS‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

New Phytologist, Journal Year: 2019, Volume and Issue: 225(1), P. 511 - 529

Published: Aug. 16, 2019

Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine-tuning traits great importance. MADS-box genes are prime candidates for this, as they involved in virtually all aspects plant development. Here, we present detailed overview phylogeny and expression 201 MIKC-type genes. Homoeolog retention significantly above average genome-wide rate genes, indicating that many homoeologs functionally not redundant. Gene generally agreement expected subfamily-specific pattern, broad conservation function during evolution. We also found extensive expansion some subfamilies, especially those potentially adaptation to different environmental conditions like flowering time Duplications prominent distal telomeric regions. A number show novel patterns respond, example, biotic stress, pointing towards neofunctionalization. speculate conserved, duplicated neofunctionalized may have played an role diversity hence contributing importance staple food.

Language: Английский

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Wheat Vacuolar Iron Transporter TaVIT2 Transports Fe and Mn and Is Effective for Biofortification

PLANT PHYSIOLOGY, Journal Year: 2017, Volume and Issue: 174(4), P. 2434 - 2444

Published: July 6, 2017

Increasing the intrinsic nutritional quality of crops, known as biofortification, is viewed a sustainable approach to alleviate micronutrient deficiencies. In particular, iron deficiency anemia major global health issue, but content staple crops such wheat (Triticum aestivum) difficult change because genetic complexity and homeostasis mechanisms. To identify target genes for biofortification wheat, we functionally characterized homologs VACUOLAR IRON TRANSPORTER (VIT). The genome contains two VIT paralogs, TaVIT1 TaVIT2, which have different expression patterns are both low in endosperm. not TaVIT1, was able rescue growth yeast (Saccharomyces cerevisiae) mutant defective vacuolar transport. TaVIT2 also complemented manganese transporter zinc mutant. By overexpressing under control an endosperm-specific promoter, achieved greater than 2-fold increase white flour fractions, exceeding minimum legal fortification levels countries United Kingdom. antinutrient phytate increased fraction bioavailable vitro, suggesting that food products made from biofortified could contribute improved nutrition. single-gene impacted minimally on plant effective barley (Hordeum vulgare). Our results show by enhancing transport endosperm, this essential accumulated tissue, bypassing existing homeostatic

Language: Английский

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TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

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

Published: Dec. 1, 2019

Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent assembly efforts in the large-genome Triticeae crops wheat and barley have relied on commercial closed-source algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct scaffolds megabase-scale contiguity ordered into chromosomal pseudomolecules. evaluate performance of TRITEX publicly available tetraploid wild emmer hexaploid bread wheat, improved annotated reference cultivar Morex as a community resource.

Language: Английский

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TEOSINTE BRANCHED1 Regulates Inflorescence Architecture and Development in Bread Wheat (Triticum aestivum)

The Plant Cell, Journal Year: 2018, Volume and Issue: 30(3), P. 563 - 581

Published: Feb. 14, 2018

The flowers of major cereals are arranged on reproductive branches known as spikelets, which group together to form an inflorescence. Diversity for inflorescence architecture has been exploited during domestication increase crop yields, and genetic variation this trait potential further boost grain production. Multiple genes that regulate have identified by studying alleles modify gene activity or dosage; however, little is in wheat. Here, we show TEOSINTE BRANCHED1 (TB1) regulates bread wheat (Triticum aestivum) investigating lines display a branching "paired spikelets." We TB1 interacts with FLOWERING LOCUS T1 increased dosage alters growth rate process includes reduced expression meristem identity genes, allelic diversity found associate genetically paired spikelet development modern cultivars. propose coordinates formation axillary spikelets the vegetative floral transition function could help yields.

Language: Английский

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The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants

Cell, Journal Year: 2020, Volume and Issue: 181(5), P. 1097 - 1111.e12

Published: May 1, 2020

Language: Английский

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What Is Gluten—Why Is It Special?

Frontiers in Nutrition, Journal Year: 2019, Volume and Issue: 6

Published: July 5, 2019

Wheat gluten has an immense impact on human nutrition as it largely determines the processing properties of wheat flour, and in particular ability to make leavened breads, other baked products, pasta noodles. However, there been increasing interest over past two decades because its well-established role triggering coeliac disease, perceived adverse reactions wheat. The literature is vast extends back centuries, with most studies focusing structures proteins their determining functional flour dough. This article provides a concise account gluten, features which are relevant disease and, lesser extent, gluten-related disorders. It includes descriptions biological proteins, relationships protein families, presence related types may also contribute impacts health. therefore understanding system at level required by those health

Language: Английский

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Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Heredity, Journal Year: 2020, Volume and Issue: 125(6), P. 396 - 416

Published: July 3, 2020

Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent now play a central role. By mixing recombining genomes multiple founders, combine many commonly sought beneficial properties mapping populations. For example, they have high power resolution for quantitative trait loci, diversity minimal population structure. Many been constructed in crop species, their inbred germplasm associated phenotypic genotypic data serve as enduring resources. Their utility has grown being tool loci to means providing breeding programmes. Genomics approaches, including de novo genome assemblies gene annotations allowed imputation rich sequence information into descendent population, expanding breadth research applications Here, we report recent successes crops. We also propose an ideal genotypic, 'package' that should feature optimise use powerful community resources research, development

Language: Английский

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