Shifting the limits in wheat research and breeding using a fully annotated reference genome

Science, Journal Year: 2018, Volume and Issue: 361(6403)

Published: Aug. 17, 2018

Insights from the annotated wheat genome Wheat is one of major sources food for much world. However, because bread wheat's a large hybrid mix three separate subgenomes, it has been difficult to produce high-quality reference sequence. Using recent advances in sequencing, International Genome Sequencing Consortium presents an with detailed analysis gene content among subgenomes and structural organization all chromosomes. Examples quantitative trait mapping CRISPR-based modification show potential using this agricultural research breeding. Ramírez-González et al. exploited fruits endeavor identify tissue-specific biased expression coexpression networks during development exposure stress. These resources will accelerate our understanding genetic basis wheat. Science , issue p. eaar7191 ; see also eaar6089

Language: Английский

---

GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: March 18, 2020

Abstract An important assessment prior to genome assembly and related analyses is profiling, where the k-mer frequencies within raw sequencing reads are analyzed estimate major characteristics such as size, heterozygosity, repetitiveness. Here we introduce GenomeScope 2.0 ( https://github.com/tbenavi1/genomescope2.0 ), which applies combinatorial theory establish a detailed mathematical model of how distributed in heterozygous polyploid genomes. We describe evaluate practical implementation polyploid-aware mixture that quickly accurately infers properties across thousands simulated several real datasets spanning broad range complexity. also present method called Smudgeplot https://github.com/KamilSJaron/smudgeplot ) visualize ploidy structure by analyzing pairs. successfully apply approach systems known variable levels Meloidogyne genus extreme case octoploid Fragaria × ananassa .

Language: Английский

---

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

---

The axolotl genome and the evolution of key tissue formation regulators

Nature, Journal Year: 2018, Volume and Issue: 554(7690), P. 50 - 55

Published: Jan. 24, 2018

Abstract Salamanders serve as important tetrapod models for developmental, regeneration and evolutionary studies. An extensive molecular toolkit makes the Mexican axolotl ( Ambystoma mexicanum ) a key representative salamander investigations. Here we report sequencing assembly of 32-gigabase-pair genome using an approach that combined long-read sequencing, optical mapping development new assembler (MARVEL). We observed size expansion introns intergenic regions, largely attributable to multiplication long terminal repeat retroelements. provide evidence intron in developmental genes is under constraint species-restricted may contribute limb regeneration. The does not contain essential gene Pax3 . However, mutation paralogue Pax7 resulted phenotype was similar those seen −/− mutant mice. provides rich biological resource

Language: Английский

---

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

Nature Reviews Genetics, Journal Year: 2018, Volume and Issue: 19(6), P. 329 - 346

Published: March 29, 2018

Language: Английский

---

Genomic architecture and introgression shape a butterfly radiation

Science, Journal Year: 2019, Volume and Issue: 366(6465), P. 594 - 599

Published: Oct. 31, 2019

We used 20 de novo genome assemblies to probe the speciation history and architecture of gene flow in rapidly radiating Heliconius butterflies. Our tests distinguish incomplete lineage sorting from introgression indicate that has obscured several ancient phylogenetic relationships this group over large swathes genome. Introgressed loci are underrepresented low-recombination gene-rich regions, consistent with purging foreign alleles more tightly linked incompatibility loci. Here, we identify a hitherto unknown inversion traps color pattern switch locus. infer was transferred between lineages by is convergent similar rearrangement another part genus. These multiple sequences enable improved understanding importance selective processes adaptive radiation.

Language: Английский

---

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

---

Long-read sequence assembly: a technical evaluation in barley

The Plant Cell, Journal Year: 2021, Volume and Issue: 33(6), P. 1888 - 1906

Published: March 10, 2021

Abstract Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources often several complementary sequence genome mapping approaches. The recent development fast accurate long-read sequencing by circular consensus (CCS) on the PacBio platform may greatly increase scope pan-genome projects. Here, we compare current platforms regarding their ability to rapidly generate contiguous assemblies in studies barley (Hordeum vulgare). Most are clearly superior reference based short-reads. Assemblies derived from long reads excel most metrics, but CCS approach was cost-effective strategy for assembling tens genomes. A downsampling analysis indicated that 20-fold coverage can yield very good assemblies, while even five-fold data capture complete genes. We present an updated with near-complete representation intergenic space. Long-read underpin construction sequences multiple a species build infrastructures Triticeae crops wild relatives.

Language: Английский

---

The Rise and Rise ofNicotiana benthamiana: A Plant for All Reasons

Annual Review of Phytopathology, Journal Year: 2018, Volume and Issue: 56(1), P. 405 - 426

Published: Aug. 25, 2018

A decade ago, the value of Nicotiana benthamiana as a tool for plant molecular biologists was beginning to be appreciated. Scientists were using it study plant-microbe and protein-protein interactions, species choice with which activate plasmid-encoded viruses, screen gene functions virus-induced silencing (VIGS), transiently express genes by leaf agroinfiltration. However, little information about species’ origin, diversity, genetics, genomics available, asking question whether N. is second fiddle or virtuoso. In this review, we look at increased knowledge its applications over past decade. Although may still sidekick Arabidopsis, shines ever more brightly realized yet-to-be-exploited potential.

Language: Английский

---

Next-Generation Sequencing Technologies

Cold Spring Harbor Perspectives in Medicine, Journal Year: 2018, Volume and Issue: 9(11), P. a036798 - a036798

Published: Nov. 26, 2018

W. Richard McCombie1, John D. McPherson2 and Elaine R. Mardis3 1Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York 11797 2Department of Biochemistry Molecular Medicine, University California Davis Comprehensive Cancer Sacramento, 95817 3Institute for Genomic Medicine at Nationwide Children's Hospital, The Ohio State College Institute Columbus, 43205 Correspondence: jdmcpherson{at}ucdavis.edu

Language: Английский

---