A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value

Cell Research, Journal Year: 2017, Volume and Issue: 27(11), P. 1327 - 1340

Published: Oct. 10, 2017

Chenopodium quinoa is a halophytic pseudocereal crop that being cultivated in an ever-growing number of countries. Because highly resistant to multiple abiotic stresses and its seed has better nutritional value than any other major cereals, it regarded as future ensure global food security. We generated high-quality genome draft using inbred line the cultivar Real. The experienced one recent duplication about 4.3 million years ago, likely reflecting fusion two parents, addition γ paleohexaploidization reported for most eudicots. repetitive (64.5% repeat content) contains 54 438 protein-coding genes 192 microRNA genes, with more 99.3% having orthologous from glycophylic species. Stress tolerance associated expansion involved ion nutrient transport, ABA homeostasis signaling, enhanced basal-level responses. Epidermal salt bladder cells exhibit similar characteristics trichomes, significantly higher expression related energy import biosynthesis compared leaf lamina. sequence provides insights into exceptional evolution halophytes, enabling identification salinity tolerance, providing basis molecular breeding quinoa.

Language: Английский

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Developing naturally stress-resistant crops for a sustainable agriculture

Nature Plants, Journal Year: 2018, Volume and Issue: 4(12), P. 989 - 996

Published: Nov. 14, 2018

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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De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

The Plant Cell, Journal Year: 2017, Volume and Issue: 29(10), P. 2336 - 2348

Published: Oct. 1, 2017

Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior this, sequencing was mainly used analyze microbial samples. Here, we describe the generation a comprehensive data set with median read length 11,979 bp for self-compatible accession wild tomato species Solanum pennellii We assembly its genome contig N50 2.5 MB. The pipeline comprised initial correction Canu and SMARTdenovo. resulting raw nanopore-based de novo is structurally highly similar that reference S. LA716 but has high error rate rich homopolymer deletions. After polishing Illumina reads, obtained an <0.02% when assessed versus same gene completeness 96.53%, slightly surpassing Taken together, our indicate such long can be affordably assemble gigabase-sized plant genomes.

Language: Английский

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Designing future crops: challenges and strategies for sustainable agriculture

The Plant Journal, Journal Year: 2020, Volume and Issue: 105(5), P. 1165 - 1178

Published: Dec. 1, 2020

Summary Crop production is facing unprecedented challenges. Despite the fact that food supply has significantly increased over past half‐century, ~8.9 and 14.3% people are still suffering from hunger malnutrition, respectively. Agricultural environments continuously threatened by a booming world population, shortage of arable land, rapid changes in climate. To ensure ecosystem security, there need to design future crops for sustainable agriculture development maximizing net minimalizing undesirable effects on environment. The projects, recently launched National Natural Science Foundation China Chinese Academy Sciences (CAS), aim develop roadmap customized using cutting‐edge technologies Breeding 4.0 era. In this perspective, we first introduce background missions these projects. We then outline strategies crops, such as improvement current well‐cultivated de novo domestication wild species redomestication cultivated crops. further discuss how ambitious goals can be achieved recent new integrative omics tools, advanced genome‐editing tools synthetic biology approaches. Finally, summarize related opportunities challenges

Language: Английский

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A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies

Cell, Journal Year: 2020, Volume and Issue: 181(2), P. 460 - 474.e14

Published: March 18, 2020

Language: Английский

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Current Strategies of Polyploid Plant Genome Sequence Assembly

Frontiers in Plant Science, Journal Year: 2018, Volume and Issue: 9

Published: Nov. 21, 2018

Polyploidy or duplication of an entire genome occurs in the majority angiosperms. The understanding polyploid genomes is important for improvement those crops, which humans rely on sustenance and basic nutrition. As climate change continues to pose a potential threat agricultural production, there will increasingly be demand plant cultivars that can resist biotic abiotic stresses also provide needed improved In past decade, Next Generation Sequencing (NGS) has fundamentally changed genomics landscape by providing tools exploration genomes. Here, we review challenges assembly genomes, present recent advances genomic resources functional molecular genetics breeding. diploid less heterozygous progenitor species are available, discuss lack complexity these currently available reference as they relate crops. Finally, approaches haplotyping phasing impact third generation technologies assembly.

Language: Английский

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Global expansion of quinoa and challenges for the Andean region

Global Food Security, Journal Year: 2020, Volume and Issue: 26, P. 100429 - 100429

Published: Sept. 1, 2020

Language: Английский

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A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: Nov. 13, 2018

Long-read sequencing technologies have greatly facilitated assemblies of large eukaryotic genomes. In this paper, Oxford Nanopore sequences generated on a MinION sequencer are combined with Bionano Genomics Direct Label and Stain (DLS) optical maps to generate chromosome-scale de novo assembly the repeat-rich Sorghum bicolor Tx430 genome. The final consists 29 scaffolds, encompassing in most cases entire chromosome arms. It has scaffold N50 33.28 Mbps covers 90% expected genome length. A sequence accuracy 99.85% is obtained after aligning against Illumina data 99.6% 34,211 public gene models align assembly. Comparisons BTx623 DLS v3.0.1 suggest substantial discrepancies whose origin remains be determined. summary, study demonstrates that informative complex plant genomes can by combining nanopore maps.

Language: Английский

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Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

Systematic Biology, Journal Year: 2020, Volume and Issue: 70(2), P. 219 - 235

Published: June 12, 2020

Abstract Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, well model violation, errors processing, orthology inference, gene estimation. Species methods that identify accommodate all sources of conflict are not available, but a combination multiple approaches help tease apart alternative conflict. Here, using phylotranscriptomic analysis with reference genomes, we test hypothesis ancient hybridization events within the plant family Amaranthaceae s.l. was previously supported morphological, ecological, Sanger-based molecular data. The set included seven genomes 88 transcriptomes, 17 generated for this study. We examined gene-tree coalescent-based species trees network analyses, site pattern tests introgression, topology tests, synteny simulations. found might have high levels backbone Furthermore, evidence three consecutive short internal branches produce anomalous contributing to discordance. Overall, our results suggest product an rapid diversification, remains, probably will remain, unresolved. This work highlights potential problems identifiability associated including, particular, phylogenetic methods. Our also demonstrate importance thoroughly testing phylogenomic especially context ancient, radiations. provide several recommendations exploring conflicting signals situations. [Amaranthaceae; discordance; hybridization; sorting; phylogenomics; network; tree; transcriptomics.]

Language: Английский

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