Mineral resource reviews, Journal Year: 2020, Volume and Issue: unknown, P. 155 - 181
Published: Dec. 7, 2020
Language: Английский
Nature, Journal Year: 2020, Volume and Issue: 588(7837), P. 277 - 283
Published: Nov. 25, 2020
Abstract Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts wheat ( Triticum spp.) been more challenging. This is largely owing to size and complexity genome 1 , lack genome-assembly data for multiple lines 2,3 . Here we generated ten chromosome pseudomolecule five scaffold assemblies hexaploid explore genomic diversity among from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions wild relatives differences gene content resulting complex histories aimed at improving adaptation diverse environments, grain yield quality, resistance stresses 4,5 We provide examples outlining utility these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved disease characterization Sm1 6 associated with insect resistance. These will basis functional discovery deliver next generation modern cultivars.
Language: Английский
Citations
736
Nature Ecology & Evolution, Journal Year: 2021, Volume and Issue: 5(10), P. 1367 - 1381
Published: Aug. 19, 2021
Abstract Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form ‘genome shock’, such as genome reorganization and subgenome expression dominance. Here we study in Arabidopsis suecica , a post-glacial allopolyploid species formed via hybridization thaliana arenosa . We generated chromosome-level assembly A. complemented it with polymorphism transcriptome data from all species. Despite divergence around 6 million years ago (Ma) between the ancestral differences their composition, see no evidence shock: colinear genomes; there dominance expression; transposon dynamics appear stable. However, find changes suggesting gradual adaptation polyploidy. In particular, shows upregulation meiosis-related genes, possibly prevent aneuploidy undesirable homeologous exchanges that are observed synthetic cyto-nuclear processes, response new cytoplasmic environment plastids maternally inherited These not seen hybrids, thus likely represent subsequent evolution.
Language: Английский
Citations
87
Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)
Published: July 26, 2022
The fungus Blumeria graminis f. sp. tritici causes wheat powdery mildew disease. Here, we study its spread and evolution by analyzing a global sample of 172 genomes. Our analyses show that B.g. emerged in the Fertile Crescent during domestication. After it throughout Eurasia, colonization brought to America, where hybridized with unknown grass species. Recent trade USA strains Japan, European China. In both places, they local ancestral strains. Thus, although spreads wind regionally, our results indicate humans drove history rapidly evolved through hybridization.
Language: Английский
Citations
51
Plant Biotechnology Journal, Journal Year: 2019, Volume and Issue: 18(3), P. 814 - 828
Published: Sept. 3, 2019
The diploid wild cotton species Gossypium australe possesses excellent traits including resistance to disease and delayed gland morphogenesis, has been successfully used for distant breeding programmes incorporate into domesticated cotton. Here, we sequenced the G. genome by integrating PacBio, Illumina short read, BioNano (DLS) Hi-C technologies, acquired a high-quality reference with contig N50 of 1.83 Mb scaffold 143.60 Mb. We found that 73.5% is composed various repeat sequences, differing from those arboreum (85.39%), hirsutum (69.86%) barbadense (69.83%). showed closer collinear relationships than raimondii undergone less extensive reorganization genome. Selection signature transcriptomics analyses implicated multiple genes in responses, GauCCD7 GauCBP1, experiments revealed induction both Verticillium dahliae plant hormones strigolactone (GR24), salicylic acid (SA) methyl jasmonate (MeJA). Experiments using Verticillium-resistant cultivar confirmed knockdown homologues these caused significant reduction against dahliae. Moreover, newly identified gland-associated gene GauGRAS1 glandless phenotype partial tissues australe. represents valuable resource research relative as well understanding evolutionary history crop genomes.
Language: Английский
Citations
73
Current Biology, Journal Year: 2020, Volume and Issue: 30(12), P. 2260 - 2274.e6
Published: May 8, 2020
Although domesticated goldfish strains exhibit highly diversified phenotypes in morphology, the genetic basis underlying these is poorly understood. Here, based on analysis of transposable elements allotetraploid genome, we found that its two subgenomes have evolved asymmetrically since a whole-genome duplication event ancestor and common carp. We conducted sequencing 27 wild goldfish. identified more than 60 million variations established population structure major strains. Genome-wide association studies strain-specific variants revealed loci associated with several phenotypes, including dorsal fin loss, long-tail, telescope-eye, albinism, heart-shaped tail. Our results suggest accumulated mutations led to generation diverse domestication history. This study key resource for understanding phenotypic diversity among
Language: Английский
Citations
67
Nature Ecology & Evolution, Journal Year: 2021, Volume and Issue: 5(10), P. 1382 - 1393
Published: Aug. 19, 2021
During evolution successful allopolyploids must overcome 'genome shock' between hybridizing species but the underlying process remains elusive. Here, we report concerted genomic and epigenomic changes in resynthesized natural Arabidopsis suecica (TTAA) allotetraploids derived from thaliana (TT) arenosa (AA). A. shows conserved gene synteny content with more family gain loss A T subgenomes than respective progenitors, although arenosa-derived subgenome has structural variation transposon distributions thaliana-derived subgenome. These balanced variations are accompanied by pervasive convergent DNA methylation expression among allotetraploids. The is hypomethylated rapidly F1 to convergently T-subgenome level suecica, despite many other methylated loci being inherited all methylation, including small RNAs, may affect phenotypic variation, flowering, silencing of self-incompatibility upregulation meiosis- mitosis-related genes. In conclusion, improve stability adaptation during polyploid evolution.
Language: Английский
Citations
55
Current Opinion in Plant Biology, Journal Year: 2022, Volume and Issue: 69, P. 102292 - 102292
Published: Sept. 2, 2022
The prevalence of polyploidy in wild and crop species has stimulated debate over its evolutionary advantages disadvantages. Previous studies have focused on changes occurring at the polyploidization events, including genome-wide termed "genome shock," as well ancient polyploidy. Recent bioinformatics advances empirical Arabidopsis wheat relatives are filling a research gap: functional study polyploid using RNA-seq, DNA polymorphism, epigenomics. Polyploid can become generalists natura through environmental robustness by inheriting merging parental stress responses. Their evolvability is enhanced mutational working inherited standing variation. identification key genes responsible for gradual adaptive evolution will encourage synthetic biological approaches to transfer other species.
Language: Английский
Citations
36
Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(2)
Published: Jan. 26, 2022
Whole-genome duplication (polyploidization) is among the most dramatic mutational processes in nature, so understanding how natural selection differs polyploids relative to diploids an important goal. Population genetics theory predicts that recessive deleterious mutations accumulate faster allopolyploids than due masking effect of redundant gene copies, but this prediction hitherto unconfirmed. Here, we use cotton genus (Gossypium), which contains seven derived from a single polyploidization event 1-2 Million years ago, investigate mutation accumulation. We two methods identifying at nucleotide and amino acid level, along with whole-genome resequencing 43 individuals spanning six allopolyploid species their diploid progenitors, demonstrate progenitors. find that, unlike what would be expected under models demographic changes alone, strongly show biggest difference between ploidy levels, diminishes for moderately mildly mutations. further proportion nonsynonymous are coresident subgenomes allopolyploids, suggesting homoeologous acts unequally subgenomes. Our results provide genome-wide perspective on classic notions significance likely broadly applicable implications our evolutionary fate Finally, note some measures (e.g., dN/dS, πN/πS) may biased when different levels compared.
Language: Английский
Citations
30
Advanced Science, Journal Year: 2019, Volume and Issue: 7(4)
Published: Nov. 28, 2019
Like many important crops, peanut is a polyploid that underwent polyploidization, evolution, and domestication. The wild allotetraploid species Arachis monticola (A. monticola) an unique link from the diploid to cultivated tetraploid in lineage. However, little known about A. its role evolution domestication of this crop. A fully annotated sequence ≈2.6 Gb genome comparative genomics reported. Genomic reconstruction 17 diploids AA, BB, EE, KK, CC groups 30 tetraploids demonstrates monophyletic origin B subgenomes peanuts. undergo asymmetric subgenome including homoeologous exchanges, homoeolog expression bias, structural variation (SV), leading functional divergence during Significantly, SV-associated homoeologs tend show bias correlation with pod size increase tetraploids. Moreover, genomic analysis disease resistance genes shows alleles present can be introduced into breeding programs improve some traits These resources are valuable for studying domestication, improvement production resistance.
Language: Английский
Citations
54
PLoS Genetics, Journal Year: 2019, Volume and Issue: 15(2), P. e1007949 - e1007949
Published: Feb. 15, 2019
Allopolyploidy is generally perceived as a major source of evolutionary novelties and an instantaneous way to create isolation barriers. However, we do not have clear understanding how two subgenomes evolve interact once they fused in allopolyploid species nor isolated are from their relatives. Here, address these questions by analyzing genomic transcriptomic data allotetraploid Capsella bursa-pastoris three differentiated populations, Asia, Europe, the Middle East. We phased subgenomes, one descended outcrossing highly diverse grandiflora (CbpCg) other selfing genetically depauperate orientalis (CbpCo). For each subgenome, assessed its relationship with diploid relatives, temporal changes effective population size (Ne), signatures positive negative selection, gene expression patterns. In all regions, Ne decreased gradually over time CbpCo subgenome accumulated more deleterious than CbpCg. There were signs widespread admixture between C. The impacted differentially depending on geographic region suggesting either strong interploidy flow or multiple origins bursa-pastoris. Selective sweeps common CbpCg Europe East, Asia. contrast, differences limited slightly expressed Middle-East. summary, after 100,000 generations co-existence, still retained signature parental legacy but trajectory strongly varied across regions.
Language: Английский
Citations
52