Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

BMC Bioinformatics, Journal Year: 2018, Volume and Issue: 19(1)

Published: Nov. 29, 2018

Recent developments in third-gen long read sequencing and diploid-aware assemblers have resulted the rapid release of numerous reference-quality assemblies for diploid genomes. However, assembly highly heterozygous genomes is still problematic when regional heterogeneity so high that haplotype homology not recognised during assembly. This results duplication rather than consolidation into allelic variants can cause issues with downstream analysis, example variant discovery, or reconstruction using unpaired contigs.A new pipeline-Purge Haplotigs-was developed specifically sequencing-based to automate reassignment contigs, assist manual curation genome assemblies. The pipeline uses a draft haplotype-fused assembly, alignments, repeat annotations identify primary was tested on simulated dataset four recent (phased) de novo from third-generation long-read sequencing, compared similar tool. After processing Purge Haplotigs, haploid were less duplicated minimal impact completeness, had more pairings contigs.Purge Haplotigs improves representations based by identifying reassigning contigs. implementation fast scales well large genomes, it likely over-purge repetitive paralogous elements alignment-only methods. software available at https://bitbucket.org/mroachawri/purge_haplotigs under permissive MIT licence.

Language: Английский

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The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

Nature Genetics, Journal Year: 2019, Volume and Issue: 51(5), P. 865 - 876

Published: May 1, 2019

High oil and protein content make tetraploid peanut a leading food legume. Here we report high-quality genome sequence, comprising 2.54 Gb with 20 pseudomolecules 83,709 protein-coding gene models. We characterize functional groups implicated in seed size evolution, content, disease resistance symbiotic nitrogen fixation. The B subgenome has more genes general expression dominance, temporally associated long-terminal-repeat expansion the A that also raises questions about A-genome progenitor. polyploid provided insights into evolution of Arachis hypogaea other legume chromosomes. Resequencing 52 accessions suggests independent domestications formed ecotypes. Whereas 0.42–0.47 million years ago (Ma) polyploidy constrained genetic variation, sequence aids mapping candidate-gene discovery for traits such as color, foliar others, providing cornerstone genomics improvement. High-quality cultivated models provides mechanisms underlying leaf peanut.

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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Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps

Nature Plants, Journal Year: 2018, Volume and Issue: 4(11), P. 879 - 887

Published: Oct. 24, 2018

Language: Английский

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Genomic innovation for crop improvement

Nature, Journal Year: 2017, Volume and Issue: 543(7645), P. 346 - 354

Published: March 1, 2017

Language: Английский

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Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

Nature Genetics, Journal Year: 2018, Volume and Issue: 50(9), P. 1289 - 1295

Published: July 23, 2018

Abstract Maize is an important crop with a high level of genome diversity and heterosis. The sequence typical female line, B73, was previously released. Here, we report de novo assembly corresponding male representative Mo17. More than 96.4% the 2,183 Mb assembled can be accounted for by 362 scaffolds in ten pseudochromosomes 38,620 annotated protein-coding genes. Comparative analysis revealed large gene-order gene structural variations: approximately 10% genes were mutually nonsyntenic, more 20% predicted had either large-effect mutations or variations, which might cause considerable protein divergence between two inbred lines. Our study provides high-quality reference-genome maize germplasm, intraspecific order variations identified should have implications heterosis evolution.

Language: Английский

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Salt stress under the scalpel – dissecting the genetics of salt tolerance

The Plant Journal, Journal Year: 2018, Volume and Issue: 97(1), P. 148 - 163

Published: Dec. 13, 2018

Summary Salt stress limits the productivity of crops grown under saline conditions, leading to substantial losses yield in soils and brackish irrigation. tolerant could alleviate these while both increasing irrigation opportunities reducing agricultural demands on dwindling freshwater resources. However, despite significant efforts, progress towards this goal has been limited, largely because genetic complexity salt tolerance for agronomically important yield‐related traits. Consequently, focus is shifting study traits that contribute overall tolerance, thus breaking down into components are more genetically tractable. Greater consideration plasticity mechanisms throughout development across environmental conditions furthers dissection. The demand sophisticated comprehensive methodologies being met by parallel advances high‐throughput phenotyping sequencing technologies enabling multivariate characterisation vast germplasm Alongside steady improvements statistical genetics models, forward approaches elucidating gaining momentum. Subsequent quantitative trait locus gene validation also become accessible, most recently through advanced techniques molecular biology genomic analysis, facilitating translation findings field. Besides fuelling improvement established crop species, facilitates domestication naturally orphan crops. Taken together, herald a promising era discovery research plants.

Language: Английский

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Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity

GigaScience, Journal Year: 2017, Volume and Issue: 7(2)

Published: Dec. 13, 2017

Although draft genomes are available for most agronomically important plant species, the majority incomplete, highly fragmented, and often riddled with assembly scaffolding errors. These issues hinder advances in tool development functional genomics systems biology.Here we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This has contig N50 length ∼7.9 million base pairs (Mb), representing ∼300-fold improvement previous version. The vast (>99.8%) was anchored 7 pseudomolecules 2 sets optical maps Bionano Genomics. obtained ∼24.96 Mb sequence not present version F. vesca produced an improved annotation that includes 1496 new genes. Comparative syntenic analyses uncovered numerous, large-scale errors each chromosome previously published genome.Our results highlight need improve existing short-read based Furthermore, demonstrate how quality impacts commonly used addressing both fundamental applied biological questions.

Language: Английский

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Quinoa Abiotic Stress Responses: A Review

Plants, Journal Year: 2018, Volume and Issue: 7(4), P. 106 - 106

Published: Nov. 29, 2018

Quinoa (Chenopodium quinoa Willd.) is a genetically diverse Andean crop that has earned special attention worldwide due to its nutritional and health benefits ability adapt contrasting environments, including nutrient-poor saline soils drought stressed marginal agroecosystems. Drought salinity are the abiotic stresses most studied in quinoa; however, studies of other important stress factors, such as heat, cold, heavy metals, UV-B light irradiance, severely limited. In last few decades, incidence been accentuated by increase unpredictable weather patterns. Furthermore, habitually occur combinations two or more. The goals this review to: (1) provide an in-depth description existing knowledge quinoa's tolerance different stressors; (2) summarize physiological responses these (3) describe novel advances molecular tools can aid our understanding mechanisms underlying tolerance.

Language: Английский

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“La Vie en Rose”: Biosynthesis, Sources, and Applications of Betalain Pigments

Molecular Plant, Journal Year: 2017, Volume and Issue: 11(1), P. 7 - 22

Published: Dec. 26, 2017

Language: Английский

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