A route to de novo domestication of wild allotetraploid rice

Cell, Journal Year: 2021, Volume and Issue: 184(5), P. 1156 - 1170.e14

Published: Feb. 5, 2021

Language: Английский

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Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa

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

Published: May 19, 2020

Abstract Artificially improving traits of cultivated alfalfa ( Medicago sativa L.), one the most important forage crops, is challenging due to lack a reference genome and an efficient editing protocol, which mainly result from its autotetraploidy self-incompatibility. Here, we generate allele-aware chromosome-level assembly for consisting 32 allelic chromosomes by integrating high-fidelity single-molecule sequencing Hi-C data. We further establish CRISPR/Cas9-based protocol on basis this precisely introduce tetra-allelic mutations into null mutants that display obvious phenotype changes. The mutated alleles phenotypes can be stably inherited in generations transgene-free manner cross pollination, may help bypassing debate about transgenic plants. presented provide key foundations accelerating research molecular breeding crop.

Language: Английский

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GWAS: Fast-forwarding gene identification and characterization in temperate Cereals: lessons from Barley – A review

Journal of Advanced Research, Journal Year: 2019, Volume and Issue: 22, P. 119 - 135

Published: Nov. 4, 2019

Understanding the genetic complexity of traits is an important objective small grain temperate cereals yield and adaptation improvements. Bi-parental quantitative trait loci (QTL) linkage mapping a powerful method to identify regions that co-segregate in interest within research population. However, recently, association or disequilibrium (LD) using genome-wide study (GWAS) became approach for unraveling molecular basis underlying natural phenotypic variation. Many causative allele(s)/loci have been identified power this which had not detected QTL populations. In barley (Hordeum vulgare L.), GWAS has successfully applied define can be used breeding crop improvement. This promising represents tremendous step forward analysis undoubtedly proved it valuable tool identification candidate genes. review, we describe recently analyses (linkage mapping), then provide basic statistical concepts GWAS, subsequently highlight discoveries GWAS. The review explained how gene(s) state-of-art bioinformatic tools.

Language: Английский

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Benchmarking of long-read assemblers for prokaryote whole genome sequencing

F1000Research, Journal Year: 2021, Volume and Issue: 8, P. 2138 - 2138

Published: Feb. 1, 2021

Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled – one contig per chromosome or plasmid. However, the high per-read error rate of necessitates different approaches assembly than those used short-read sequencing. Multiple tools (assemblers) exist, which use a variety algorithms assembly. Methods: We 500 simulated read 120 real assess performance eight assemblers (Canu, Flye, Miniasm/Minipolish, NECAT, NextDenovo/NextPolish, Raven, Redbean Shasta) across wide parameters. Assemblies were assessed on their structural accuracy/completeness, sequence identity, circularisation computational resources used. Results: Canu v2.1 produced reliable assemblies was good with plasmids, but it performed poorly had longest runtimes all tested. Flye v2.8 also made smallest errors, though RAM. Miniasm/Minipolish v0.3/v0.1.3 likely produce clean circularisation. NECAT v20200803 at tended make larger errors. NextDenovo/NextPolish v2.3.1/v1.3.1 bad plasmid assembly. Raven v1.3.0 assembly, did not perform well small plasmids issues. v2.5 Shasta v0.7.0 computationally efficient more incomplete assemblies. Conclusions: Of tested, best overall. no single tool metrics, highlighting need continued development algorithms.

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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Benchmarking of long-read assemblers for prokaryote whole genome sequencing

F1000Research, Journal Year: 2019, Volume and Issue: 8, P. 2138 - 2138

Published: Dec. 23, 2019

Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled – one contig per chromosome or plasmid. However, the high per-read error rate of necessitates different approaches assembly than those used short-read sequencing. Multiple tools (assemblers) exist, which use a variety algorithms assembly. Methods: We 500 simulated read 120 real assess performance six assemblers (Canu, Flye, Miniasm/Minipolish, Raven, Redbean Shasta) across wide parameters. Assemblies were assessed on their structural accuracy/completeness, sequence identity, circularisation computational resources used. Results: Canu v1.9 produced moderately reliable assemblies but had longest runtimes all tested. Flye v2.6 was more did particularly well with plasmid assembly. Miniasm/Minipolish v0.3 only assembler consistently clean circularisation. Raven v0.0.5 assembly, though it not perform small plasmids issues. v2.5 Shasta v0.3.0 computationally efficient likely produce incomplete assemblies. Conclusions: Of tested, performed best overall. no single tool metrics, highlighting need continued development algorithms.

Language: Английский

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Haplotype-resolved genome analyses of a heterozygous diploid potato

Nature Genetics, Journal Year: 2020, Volume and Issue: 52(10), P. 1018 - 1023

Published: Sept. 28, 2020

Abstract Potato ( Solanum tuberosum L.) is the most important tuber crop worldwide. Efforts are underway to transform from a clonally propagated tetraploid into seed-propagated, inbred-line-based hybrid, but this process requires better understanding of potato genome. Here, we report 1.67-Gb haplotype-resolved assembly diploid potato, RH89-039-16, using combination multiple sequencing strategies, including circular consensus sequencing. Comparison two haplotypes revealed ~2.1% intragenomic diversity, 22,134 predicted deleterious mutations in 10,642 annotated genes. In 20,583 pairs allelic genes, 16.6% and 30.8% exhibited differential expression methylation between alleles, respectively. Deleterious differentially expressed alleles were dispersed throughout both haplotypes, complicating strategies eradicate or stack beneficial via meiotic recombination. This study offers holistic view genome organization species provides insights technological evolution resolving complex genomes.

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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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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A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)

Published: March 13, 2020

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently two component subgenomes (putatively deriving from C. canephora and eugenioides) perform a genome-wide analysis genetic diversity in cultivated coffee germplasm wild populations growing center origin species. We assembled total length 1.536 Gbp, 444 Mb 527 which were assigned eugenioides subgenomes, respectively, predicted 46,562 gene models, 21,254 22,888 eugeniodes subgenome, respectively. Through SNP genotyping 736 accessions, we analyzed its relationship with geographic distribution historical records. observed weak population structure due low-frequency derived alleles highly negative values Taijma's D, suggesting recent severe bottleneck, most likely resulting single event polyploidization, not only for but also entire This conclusion is strongly supported by forward simulations mutation accumulation. However, PCA revealed cline reflecting west-to-east geographical East Africa Arabian Peninsula. extremely low levels variation species, as consequence polyploidization event, make exploitation within breeding purposes less interesting than crop stress need introgression new variability diploid progenitors.

Language: Английский

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