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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Sequencing DNA with nanopores: Troubles and biases

PLoS ONE, Journal Year: 2021, Volume and Issue: 16(10), P. e0257521 - e0257521

Published: Oct. 1, 2021

Oxford Nanopore Technologies' (ONT) long read sequencers offer access to longer DNA fragments than previous sequencer generations, at the cost of a higher error rate. While many papers have studied correction methods, few addressed detailed characterization observed errors, task complicated by frequent changes in chemistry and software ONT technology. The MinION is now more stable this paper proposes an up-to-date view its landscape, using most mature flowcell basecaller. We sequencing biases on both bacterial human reads. found that, although expected not suffer from GC bias, it crucial parameter with respect errors. In particular, low-GC reads fewer errors high-GC (about 6% 8% respectively). profile for homopolymeric regions or short repeats, source about half all also depends rate mainly shows deletions, there are some insertions. Another interesting finding that quality measure, over-estimated, offers valuable information predict as well abundance supplemented study analysis rapeseed RNA set shown level deletion these data. Finally, we implemented open pipeline long-term monitoring profile, which enables users easily compute various presented work, including future developments device. Overall, hope work will provide basis design better error-correction methods.

Language: Английский

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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

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Twenty years of plant genome sequencing: achievements and challenges

Trends in Plant Science, Journal Year: 2021, Volume and Issue: 27(4), P. 391 - 401

Published: Nov. 12, 2021

Language: Английский

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How the pan-genome is changing crop genomics and improvement

Genome biology, Journal Year: 2021, Volume and Issue: 22(1)

Published: Jan. 4, 2021

Abstract Crop genomics has seen dramatic advances in recent years due to improvements sequencing technology, assembly methods, and computational resources. These have led the development of new tools facilitate crop improvement. The study structural variation within species characterization pan-genome revealed extensive genome content among individuals a that is paradigm shifting Here, we review how utilization these light pan-genomes are becoming available for many species.

Language: Английский

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A complete telomere-to-telomere assembly of the maize genome

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(7), P. 1221 - 1231

Published: June 15, 2023

Abstract A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of genomic research. Through generating deep coverage ultralong Oxford Nanopore Technology (ONT) and PacBio HiFi reads, we report here a assembly maize with each chromosome entirely traversed in single contig. The 2,178.6 Mb T2T Mo17 base accuracy over 99.99% unveiled structural features all repetitive regions genome. There were several super-long simple-sequence-repeat arrays having consecutive thymine–adenine–guanine (TAG) tri-nucleotide repeats up to 235 kb. entire nucleolar organizer region 26.8 array 2,974 45S rDNA copies revealed enormously complex patterns duplications transposon insertions. Additionally, assemblies ten centromeres enabled us precisely dissect repeat compositions both CentC-rich CentC-poor centromeres. represents major step forward understanding complexity highly recalcitrant higher plant genomes.

Language: Английский

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Green plant genomes: What we know in an era of rapidly expanding opportunities

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(4)

Published: Jan. 18, 2022

Green plants play a fundamental role in ecosystems, human health, and agriculture. As de novo genomes are being generated for all known eukaryotic species as advocated by the Earth BioGenome Project, increasing genomic information on green land is essential. However, setting standards generation storage of complex set that characterize lineage life major challenge plant scientists. Such will need to accommodate immense variation genome size, transposable element content, structural complexity while enabling research into molecular evolutionary processes have resulted this enormous variation. Here we provide an overview assessment current state knowledge genomes. To date fewer than 300 complete chromosome-scale assemblies representing 900 been across estimated 450,000 500,000 clade. These range size from 12 Mb 27.6 Gb biased toward agricultural crops with large branches tree untouched genomic-scale sequencing. Locating suitable tissue samples most plants, especially those taxa extreme environments, remains one biggest hurdles our inventory. Furthermore, annotation at present undergoing intensive improvement. It hope fresh help development quality cohesive meaningful synthesis scale up future.

Language: Английский

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The integrated genomics of crop domestication and breeding

Cell, Journal Year: 2022, Volume and Issue: 185(15), P. 2828 - 2839

Published: May 27, 2022

Language: Английский

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Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

Nature Methods, Journal Year: 2022, Volume and Issue: 19(6), P. 687 - 695

Published: March 31, 2022

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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