Structural variation (SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(4), P. 678 - 693

Published: Feb. 9, 2023

Structural variations (SVs) have long been described as being involved in the origin, adaption, and domestication of species. However, underlying genetic genomic mechanisms are poorly understood. Here, we report a high-quality genome assembly Gossypium barbadense acc. Tanguis, landrace that is closely related to formation extra-long-staple (ELS) cultivated cotton. An SV-based pan-genome (Pan-SV) was then constructed using total 182 593 non-redundant SVs, including 2236 inversions, 97 398 insertions, 82 959 deletions from 11 assembled genomes allopolyploid The utility this Pan-SV demonstrated through population structure analysis genome-wide association studies (GWASs). Using segregation mapping populations produced crossing ELS cotton along with an GWAS, certain SVs responsible for speciation, domestication, improvement tetraploid cottons were identified. Importantly, some presently identified associated yield fiber quality had not previous SNP-based GWAS. In particular, 9-bp insertion or deletion found associate elimination interspecific reproductive isolation between hirsutum G. barbadense. Collectively, study provides new insights into genome-wide, gene-scale linked important agronomic traits major crop species highlights importance during

Language: Английский

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Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance

Nature Genetics, Journal Year: 2024, Volume and Issue: 56(4), P. 710 - 720

Published: March 15, 2024

Abstract Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of bamboo system (Poaceae: Bambusoideae) comprising series lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies 476 transcriptome samples. We find that woody subgenomes exhibit stunning karyotype stability, parallel dominance two clades gradual shift clade. Allopolyploidization have shaped evolution tree-like lignified culms, rapid growth synchronous flowering characteristic bamboos as large grasses. Our work provides insights into remarkable system, including its dependence on genomic context ability switch which dominant over evolutionary time.

Language: Английский

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Uptake and effect of carboxyl-modified polystyrene microplastics on cotton plants

Journal of Hazardous Materials, Journal Year: 2024, Volume and Issue: 466, P. 133581 - 133581

Published: Jan. 22, 2024

Language: Английский

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Evolutionary dynamics of mitochondrial genomes and intracellular transfers among diploid and allopolyploid cotton species

BMC Biology, Journal Year: 2025, Volume and Issue: 23(1)

Published: Jan. 10, 2025

Plant mitochondrial genomes (mitogenomes) exhibit extensive structural variation yet extremely low nucleotide mutation rates, phenomena that remain only partially understood. The genus Gossypium, a globally important source of cotton, offers wealth long-read sequencing resources to explore mitogenome and plastome dynamics accompanying the evolutionary divergence its approximately 50 diploid allopolyploid species. Here, we assembled 19 mitogenomes from Gossypium species, representing all genome groups (diploids A through G, K, allopolyploids AD) based on uniformly applied strategy. graph-based assembly method revealed more alternative conformations than previously recognized, some which confirmed structure reported in earlier studies cotton. Using data, quantified mediated by recombination events between repeats, phylogenetically informative variants were noted. Nucleotide substitution rate comparisons coding non-coding regions rates across entire mitogenome. Genome-wide mapping nuclear organellar DNA transfers (NUOTs) nonrandom distribution genome. In fate NUOT varied, with mitochondrion-to-nucleus transfer (NUMT) predominantly retained as short fragments genome, plastid sequences integrated into nucleus. Phylogenetic relationships inferred using different data sets highlighted distinct histories among these cellular compartments, providing ancillary evidence relevant history Gossypium. comprehensive analysis demonstrates complex reveals three throughout cotton genus. findings enhance our general understanding evolution, comparative inter-compartment genomic integration.

Language: Английский

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The miR319-Targeted GhTCP4 Promotes the Transition from Cell Elongation to Wall Thickening in Cotton Fiber

Molecular Plant, Journal Year: 2020, Volume and Issue: 13(7), P. 1063 - 1077

Published: May 16, 2020

Plant cell growth involves a complex interplay among cell-wall expansion, biosynthesis, and, in specific tissues, secondary wall (SCW) deposition, yet the coordination of these processes remains elusive. Cotton fiber cells are developmentally synchronous, highly elongated, and contain nearly pure cellulose when mature. Here, we report that transcription factor GhTCP4 plays an important role balancing cotton elongation synthesis. During development expression miR319 declines while transcript levels increase, with high latter promoting SCW deposition. interacts homeobox-containing factor, GhHOX3, repressing its transcriptional activity. GhHOX3 function antagonistically to regulate elongation, thereby establishing temporal control transition stage. We found overexpression GhTCP4A upregulated accelerated activation biosynthetic pathway cells, as revealed by transcriptome promoter activity analyses, resulting shorter fibers varied lengths thicker walls. In contrast, downregulation led slightly longer thinner The GhHOX3-GhTCP4 may represent general mechanism cellular plants since both conserved factors many species, thus providing us potential molecular tool for design traits.

Language: Английский

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Integrating multi-omics data for crop improvement

Journal of Plant Physiology, Journal Year: 2020, Volume and Issue: 257, P. 153352 - 153352

Published: Dec. 17, 2020

Our agricultural systems are now in urgent need to secure food for a growing world population. To meet this challenge, we better characterization of plant genetic and phenotypic diversity. The combination genomics, transcriptomics metabolomics enables deeper understanding the mechanisms underlying complex architecture many traits relevance. We review recent advances genomics see how these can be integrated with broad molecular profiling approaches improve our variation inform crop breeding strategies.

Language: Английский

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CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research

Plants, Journal Year: 2021, Volume and Issue: 10(12), P. 2805 - 2805

Published: Dec. 18, 2021

Over the last eight years, volume of whole genome, gene expression, SNP genotyping, and phenotype data generated by cotton research community has exponentially increased. The efficient utilization/re-utilization these complex large datasets for knowledge discovery, translation, application in crop improvement requires them to be curated, integrated with other types data, made available access analysis through online search tools. Initiated 2012, CottonGen is an database providing peer-reviewed genomic, genetic, breeding Used researchers worldwide, managed experts crop-specific knowledge, it continuous logical choice integrate new provide necessary interfaces information retrieval. repository contains colleague, gene, genotype, germplasm, map, marker, metabolite, phenotype, publication, QTL, species, transcriptome, trait curated team. number entries housed increased dramatically, example, since 2014 there been 18-fold increase genes/mRNAs, a 23-fold genomes, 372-fold genotype data. New tools include genetic map viewer, genome browser, synteny metabolite pathways sequence retrieval, BLAST, management system (BIMS), as well various pages types. serves home International Cotton Genome Initiative, managing its elections serving communication coordination hub community. With extensive curation integration tools, will continue facilitate utilization critical resources empower improvement.

Language: Английский

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Gradual evolution of allopolyploidy in Arabidopsis suecica

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

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Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes

Genome biology, Journal Year: 2020, Volume and Issue: 21(1)

Published: July 22, 2020

Polyploidy provides new genetic material that facilitates evolutionary novelty, species adaptation, and crop domestication. often leads to an increase in cell or organism size, which may affect transcript abundance transcriptome but the relationship between polyploidy changes remains poorly understood. Plant cells undergo endoreduplication, confounding polyploid effect.

Language: Английский

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Altered chromatin architecture and gene expression during polyploidization and domestication of soybean

The Plant Cell, Journal Year: 2021, Volume and Issue: 33(5), P. 1430 - 1446

Published: March 13, 2021

Abstract Polyploidy or whole-genome duplication (WGD) is widespread in plants and a key driver of evolution speciation, accompanied by rapid dynamic changes genomic structure gene expression. The 3D the genome intricately linked to expression, but its role transcription regulation following polyploidy domestication remains unclear. Here, we generated high-resolution (∼2 kb) Hi-C maps for cultivated soybean (Glycine max), wild soja), common bean (Phaseolus vulgaris). We found polyploidization may induce architecture topologically associating domains subsequent diploidization led chromatin topology alteration around chromosome-rearrangement sites. Compared with single-copy small-scale duplicated genes, WGD genes displayed more long-range chromosomal interactions were coupled higher levels expression accessibilities void DNA methylation. Interestingly, loop reorganization was involved divergence during domestication. Genes loops under stronger artificial selection than without loops. These findings provide insights into roles structures on polyploidization, diploidization, soybean.

Language: Английский

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