Nanopore sequencing technology, bioinformatics and applications

Nature Biotechnology, Journal Year: 2021, Volume and Issue: 39(11), P. 1348 - 1365

Published: Nov. 1, 2021

Language: Английский

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De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Science, Journal Year: 2021, Volume and Issue: 373(6555), P. 655 - 662

Published: Aug. 5, 2021

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as founders maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. results demonstrate ancient tetraploid character continues to degrade by fractionation present day. Excellent contiguity over repeat arrays complete annotation centromeres revealed additional variation major cytological landmarks. show combining structural single-nucleotide polymorphisms can improve power quantitative studies. also document at level DNA methylation unmethylated regions are enriched cis-regulatory elements contribute phenotypic variation.

Language: Английский

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Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data

Nature Plants, Journal Year: 2019, Volume and Issue: 5(8), P. 833 - 845

Published: Aug. 5, 2019

Language: Английский

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SMARTdenovo: a de novo assembler using long noisy reads

Gigabyte, Journal Year: 2021, Volume and Issue: 2021, P. 1 - 9

Published: March 8, 2021

Long-read single-molecule sequencing has revolutionized

Language: Английский

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Building near-complete plant genomes

Current Opinion in Plant Biology, Journal Year: 2020, Volume and Issue: 54, P. 26 - 33

Published: Jan. 22, 2020

Plant genomes span several orders of magnitude in size, vary levels ploidy and heterozygosity, contain old recent bursts transposable elements, which render them challenging but interesting to assemble. Recent advances single molecule sequencing physical mapping technologies have enabled high-quality, chromosome scale assemblies plant species with increasing complexity size. Single reads can now exceed megabases length, providing unprecedented opportunities untangle genomic regions missed by short read technologies. However, polyploid heterozygous are still difficult assemble provide for new tools approaches. Haplotype phasing, structural variant analysis de novo pan-genomics the emerging frontiers genome assembly.

Language: Английский

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Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

Science, Journal Year: 2020, Volume and Issue: 370(6523)

Published: Dec. 18, 2020

A high-quality rhesus macaque genome Genome technology has improved substantially since the first full organismal genomes were generated. Applying new technology, Warren et al. refined of macaque, a model nonhuman primate. Long-read and other recent advances in sequencing applied to generate with far fewer gaps helped refine locations numbers repetitive elements. Furthermore, authors performed resequencing among populations identify genetic variability macaque. Thus, previously incomplete inaccurate set sequence information is now fully resolved, improving gene mapping for biomedical comparative studies. Science , this issue p. eabc6617

Language: Английский

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Extensive variation within the pan-genome of cultivated and wild sorghum

Nature Plants, Journal Year: 2021, Volume and Issue: 7(6), P. 766 - 773

Published: May 20, 2021

Language: Английский

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Genome maps across 26 human populations reveal population-specific patterns of structural variation

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: March 4, 2019

Abstract Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across experiment. Analyzing maps of 154 individuals from 26 populations sequenced 1000 Genomes Project, we find that phylogenetic population patterns similar those single nucleotide variations 86% genome, while ~2% has high complexity. We able characterize many intractable regions including segmental duplications subtelomeric, pericentromeric, acrocentric areas. In addition, discover ~60 Mb non-redundant content missing reference sequence assembly. Our results highlight need for a comprehensive set alternate haplotypes different represent SV genome.

Language: Английский

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Plant pan-genomics and its applications

Molecular Plant, Journal Year: 2022, Volume and Issue: 16(1), P. 168 - 186

Published: Dec. 15, 2022

Language: Английский

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Adapting C ₄ photosynthesis to atmospheric change and increasing productivity by elevating Rubisco content in sorghum and sugarcane

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(8)

Published: Feb. 11, 2025

Meta-analyses and theory show that with rising atmospheric [CO 2 ], Rubisco has become the greatest limitation to light-saturated leaf CO assimilation rates ( A sat ) in C 4 crops. So would transgenically increasing increase result increased productivity field? Here, we successfully overexpressed small subunit RbcS accumulation factor 1 Raf1 both sorghum sugarcane, resulting significant increases content of 13 25% up 90% respectively. 12 15% enzyme activity ~40% three independent transgenic events species. Sorghum plants also showed speeds photosynthetic induction decreased bundle sheath leakiness. These improvements translated into average 15.5% biomass field-grown a 37 81% greenhouse-grown sugarcane. This suggests potential opportunity achieve substantial this key economically important clade crops, future proofing their value under global change.

Language: Английский

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