The evolutionary significance of polyploidy

Nature Reviews Genetics, Journal Year: 2017, Volume and Issue: 18(7), P. 411 - 424

Published: May 15, 2017

Language: Английский

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Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Nature Genetics, Journal Year: 2018, Volume and Issue: 50(11), P. 1565 - 1573

Published: Oct. 8, 2018

Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of spontaneum. Sequencing a haploid S. spontaneum, AP85-441, facilitated the assembly 32 pseudo-chromosomes comprising 8 homologous groups 4 members each, bearing 35,525 genes alleles defined. The reduction basic chromosome number 10 to in spontaneum was caused by fissions 2 ancestral chromosomes followed translocations chromosomes. Surprisingly, 80% nucleotide binding site-encoding associated located rearranged 51% those regions. Resequencing 64 genomes identified balancing selection regions, maintaining their diversity. Introgressed modern randomly distributed AP85-441 genome, indicating random recombination among homologs different accessions. allele-defined genome offers new knowledge resources accelerate sugarcane improvement. sugarcane, allows prototypical version set. This reference will serve as resource

Language: Английский

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Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms

Molecular Plant, Journal Year: 2018, Volume and Issue: 11(3), P. 414 - 428

Published: Jan. 6, 2018

Language: Английский

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Simultaneous CRISPR/Cas9‐mediated editing of cassava eIF4E isoforms nCBP‐1 and nCBP‐2 reduces cassava brown streak disease symptom severity and incidence

Plant Biotechnology Journal, Journal Year: 2018, Volume and Issue: 17(2), P. 421 - 434

Published: July 19, 2018

Cassava brown streak disease (CBSD) is a major constraint on cassava yields in East and Central Africa threatens production West Africa. CBSD caused by two species of positive-sense RNA viruses belonging to the family Potyviridae, genus Ipomovirus: virus (CBSV) Ugandan (UCBSV). Diseases Potyviridae require interaction viral genome-linked protein (VPg) host eukaryotic translation initiation factor 4E (eIF4E) isoforms. encodes five eIF4E proteins: eIF4E, eIF(iso)4E-1, eIF(iso)4E-2, novel cap-binding protein-1 (nCBP-1), nCBP-2. Protein-protein experiments consistently found that VPg proteins associate with nCBPs. CRISPR/Cas9-mediated genome editing was employed generate ncbp-1, ncbp-2, ncbp-1/ncbp-2 mutants cultivar 60444. Challenge CBSV showed displayed delayed attenuated aerial symptoms, as well reduced severity incidence storage root necrosis. Suppressed symptoms were correlated titre roots relative wild-type controls. Our results demonstrate ability modify multiple genes simultaneously achieve tolerance CBSD. Future studies will investigate contribution remaining isoforms translate this knowledge into an optimized strategy for protecting from disease.

Language: Английский

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Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

Nature Genetics, Journal Year: 2017, Volume and Issue: 49(6), P. 959 - 963

Published: April 17, 2017

Cassava (Manihot esculenta Crantz) is an important staple food crop in Africa and South America; however, ubiquitous deleterious mutations may severely decrease its fitness. To evaluate these mutations, we constructed a cassava haplotype map through deep sequencing 241 diverse accessions identified >28 million segregating variants. We found that (i) although domestication has modified starch ketone metabolism pathways to allow for human consumption, the concomitant bottleneck clonal propagation have resulted large proportion of fixed amino acid changes, increased number alleles by 26%, shifted mutational burden toward common variants; (ii) been ineffectively purged, owing limited recombination genome; (iii) recent breeding efforts maintained yield masking most damaging recessive heterozygous state but unable purge mutation burden; such purging should be key target future breeding.

Language: Английский

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The interplay of demography and selection during maize domestication and expansion

Genome biology, Journal Year: 2017, Volume and Issue: 18(1)

Published: Nov. 13, 2017

The history of maize has been characterized by major demographic events, including population size changes associated with domestication and range expansion, gene flow wild relatives. interplay between selection shaped diversity across populations genomes.We investigate these processes using high-depth resequencing data from 31 landraces spanning the pre-Columbian distribution maize, four teosinte individuals (Zea mays ssp. parviglumis). Genome-wide analyses reveal that experienced pronounced declines in effective due to both a protracted bottleneck serial founder effects during post-domestication spread, while parviglumis Balsas River Valley growth. subsequent spread led an increase deleterious alleles domesticate compared progenitor. This cost is particularly Andean which more dramatic event other populations. Additionally, we detect introgression Zea mexicana into highlands Mexico, Guatemala, southwestern USA, reduces prevalence likely higher long-term teosinte.These findings underscore strong interaction historical demography efficiency illustrate how domesticated species are useful for understanding processes. landscape therefore evolutionary potential clearly influenced recent demography, factor could bear importantly on many have shifts.

Language: Английский

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A chickpea genetic variation map based on the sequencing of 3,366 genomes

Nature, Journal Year: 2021, Volume and Issue: 599(7886), P. 622 - 627

Published: Nov. 10, 2021

Abstract Zero hunger and good health could be realized by 2030 through effective conservation, characterization utilization of germplasm resources 1 . So far, few chickpea ( Cicer arietinum ) accessions have been characterized at the genome sequence level 2 Here we present a detailed map variation in 3,171 cultivated 195 wild to provide publicly available for genomics research breeding. We constructed pan-genome describe genomic diversity across its progenitor accessions. A divergence tree using genes around 80% individuals one species allowed us estimate over last 21 million years. Our analysis found chromosomal segments that show signatures selection during domestication, migration improvement. The locations deleterious mutations responsible limited genetic decreased fitness were identified elite germplasm. superior haplotypes improvement-related traits landraces can introgressed into breeding lines haplotype-based breeding, targets purging alleles genomics-assisted and/or gene editing. Finally, propose three crop strategies based on prediction enhance productivity 16 while avoiding erosion optimal contribution (OCS)-based pre-breeding. predicted performance 100-seed weight, an important yield-related trait, increased up 23% 12% with OCS- approaches, respectively.

Language: Английский

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Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(3), P. 507 - 518

Published: March 1, 2023

Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates captured 424,085 genomic structural variations (SVs). Comparative genomics transcriptomics analyses revealed the expansion of RWP-RK transcription factor family involvement endoplasmic reticulum (ER)-related genes in The overexpression gene led enhanced plant tolerance transactivated ER-related quickly, supporting roles factors ER system Furthermore, found that some SVs affected expression associated surrounding shaped adaptation during domestication population. Our study provides comprehensive resource revealing insights into laying foundation for generating more robust crops under changing climate.

Language: Английский

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Salinity responses and tolerance mechanisms in underground vegetable crops: an integrative review

Planta, Journal Year: 2022, Volume and Issue: 255(3)

Published: Feb. 15, 2022

Language: Английский

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Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 17, 2024

Abstract Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell developmental model systems, notably the genus Xenopus . Here we report a high-quality reference genome sequence for western clawed frog, tropicalis , along with draft chromosome-scale sequences three distantly related emerging frog species, Eleutherodactylus coqui Engystomops pustulosus Hymenochirus boettgeri Frog chromosomes have remained remarkably stable since Mesozoic Era, limited Robertsonian (i.e., arm-preserving) translocations end-to-end fusions found among smaller chromosomes. Conservation synteny includes conservation centromere locations, marked by centromeric tandem repeats associated Cenp-a binding surrounded pericentromeric LINE/L1 elements. This work explores structure across frogs, using dense meiotic linkage map X. chromatin conformation capture (Hi-C) data all species. Abundant satellite occupy unusually long (~20 megabase) terminal regions each chromosome coincide high rates recombination. Both embryonic differentiated cells show reproducible associations telomeres, reflecting Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral from which contemporary genomes were constructed.

Language: Английский

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