Genome-wide identification of 1R-MYB transcription factors family and functional characterization of TrMYB130 under drought stresses in Trifolium repens (L.)

Gene, Journal Year: 2025, Volume and Issue: unknown, P. 149247 - 149247

Published: Jan. 1, 2025

Language: Английский

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De novo genome assembly of white clover (Trifolium repens L.) reveals the role of copy number variation in rapid environmental adaptation

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: Aug. 7, 2024

White clover (Trifolium repens) is a globally important perennial forage legume. This species also serves as an eco-evolutionary model system for studying within-species chemical defense variation; it features well-studied polymorphism cyanogenesis (HCN release following tissue damage), with higher frequencies of cyanogenic plants favored in warmer locations worldwide. Using newly generated haplotype-resolved genome and two other long-read assemblies, we tested the hypothesis that copy number variants (CNVs) at genes play role ability white to rapidly adapt local environments. We examined questions on subgenome evolution this recently evolved allotetraploid chromosomal rearrangements broader IRLC legume clade.

Language: Английский

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Genome-wide identification and characterization of OSCA genes in white clover revealing their function in response to abiotic stresses

South African Journal of Botany, Journal Year: 2025, Volume and Issue: 178, P. 18 - 27

Published: Jan. 13, 2025

Language: Английский

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Genomic research and genetic improvement of orphan crops: novel strategies for addressing global food security challenges

Published: Jan. 1, 2025

Language: Английский

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De novo genome assembly of white clover (Trifolium repens L.) reveals the role of Copy Number Variation in rapid environmental adaptation

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 17, 2024

Abstract Background White clover ( Trifolium repens ) is a globally important perennial forage legume. This species also serves as an eco-evolutionary model system for studying within-species chemical defense variation; it features well-studied polymorphism cyanogenesis (HCN release following tissue damage), with higher frequencies of cyanogenic plants favored in warmer locations worldwide. Using newly-generated haplotype-resolved genome and two other long-read assemblies, we tested the hypothesis that copy number variants (CNVs) at genes play role ability white to rapidly adapt local environments. We examined questions on subgenome evolution this recently evolved allotetraploid chromosomal rearrangements broader IRLC legume clade. Results Integration PacBio HiFi, Omni-C, Illumina linkage map data yielded first completely de novo assembly (created without priori sequence assignment subgenomes). find has undergone extensive transposon diversification since its origin but otherwise shows highly conserved organization composition diploid progenitors; unlike some species, structure legumes. further evidence CNVs major loci; these contribute quantitative variation phenotype adaptation across wild North American populations. Conclusions study among first, our knowledge, document plant highlights value pan-genome identifying contributions structural nature.

Language: Английский

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Genetics and plasticity of white leaf mark variegation in white clover (Trifolium repens L.)

Annals of Botany, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 8, 2024

Abstract Background and Aims Leaf variegation is common in plants confers diverse adaptive functions. However, its genetic underpinnings remain largely unresolved; this particularly true for that arises through modified leaf tissue structure affects light reflection. White clover naturally polymorphic structure-based white mark variegation. It therefore provides a useful system which to examine the basis of phenotype assess potential costs photosynthetic efficiency resulting from structures. In study, we sought map loci controlling evaluate relationship between mark, thickness efficiency. Methods We generated high-density linkage an F3 mapping population, using reference genome-based single nucleotide polymorphism markers. was quantified detailed phenotypic evaluations alongside test how might affect phenotype. Mapping quantitative trait performed characterize their basis. Photosynthetic measurements were used physiological trade-offs output. Key Results The V locus, major gene responsible polymorphism, mapped distal end chromosome 5, several modifier also contribute additively intensity presence associated with greater thickness; however, increased did not detectably. Conclusions have successfully locus governing clover, along loci, revealing complex apparent absence compromised photosynthesis variegated leaves challenges notion creates fitness other This finding suggests factors maintain clover.

Language: Английский

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Centromere drive may propel the evolution of chromosome and genome size in plants

Annals of Botany, Journal Year: 2024, Volume and Issue: 134(6), P. 1067 - 1076

Published: Aug. 28, 2024

Abstract Background Genome size is influenced by natural selection and genetic drift acting on variations from polyploidy repetitive DNA sequences. We hypothesized that centromere drive, where centromeres compete for inclusion in the functional gamete during meiosis, may also affect genome chromosome size. This competition occurs asymmetric only one of four meiotic products becomes a gamete. If drive influences evolution, it impact post-polyploid diploidization, polyploid restructured to function more like diploid through chromosomal rearrangements, including fusions. tested if plant lineages with meiosis exhibit faster evolution compared those symmetric which lack as all become gametes. examined positive centromeric histone H3 (CENH3), protein can suppress frequent these lineages. Methods analysed groups different modes: gymnosperms angiosperms, bryophytes, lycophytes ferns. selected species based available CENH3 gene sequences data. Using Ornstein–Uhlenbeck evolutionary models phylogenetic regressions, we assessed rates frequency clades. Results Our analyses showed clades have higher increased Conclusions findings support hypothesis accelerates potentially influencing process diploidization. propose model single framework helps explain stability (bryophytes, ferns) its variability (gymnosperms angiosperms), providing foundation future research evolution.

Language: Английский

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A chromosome level reference genome of Diviner’s sage (Salvia divinorum) provides insight into salvinorin A biosynthesis

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Oct. 1, 2024

Language: Английский

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Signatures of selective sweeps in urban and rural white clover populations

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 3, 2024

Abstract Urbanization is increasingly recognized as a powerful force of evolutionary change. However, anthropogenic sources selection can often be similarly strong and multifarious in rural habitats, but these are ignored studies urban ecology. Despite numerous examples phenotypic differentiation between populations, we still lack an understanding the genes enabling adaptation to contrasting habitats genetic architecture underlying adaptation. In this study, conducted whole genome sequencing 120 urban, suburban, white clover plants from Toronto, Canada. We used data identify signatures selective sweeps across using both SFS haplotype-based approaches, characterize sweeps. found evidence for genomic regions involved abiotic stress tolerance growth/development populations. Urban populations did not differ proportion hard vs. soft sweeps, though were characterized by wider which may indicate differences strength or timescale selection. addition, patterns allele frequency haplotype suggest that most incomplete. These results highlight how driving ongoing motivate future work disentangling ecologically important phenotypes, estimating contemporary habitats.

Language: Английский

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The genome sequence of lesser trefoil or Irish shamrock, Trifolium dubium Sibth. (Fabaceae)

Wellcome Open Research, Journal Year: 2024, Volume and Issue: 9, P. 229 - 229

Published: April 24, 2024

We present a genome assembly from an individual Trifolium dubium (lesser trefoil; Tracheophyta; Magnoliopsida; Fabales; Fabaceae) as part of collaboration between the Darwin Tree Life and European Reference Genome Atlas. The sequence is 679.1 megabases in span. Most scaffolded into 15 chromosomal pseudomolecules. two mitochondrial genomes have lengths 133.86 kb 182.32 kb, plastid has length 126.22 kilobases.

Language: Английский

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