Haplotype-Resolved, Chromosome-Level Assembly of White Clover (<i>Trifolium repens</i> L., Fabaceae)

Santangelo, James S.; Battlay, Paul; Hendrickson, Brandon T.; Kuo, Wen-Hsi; Olsen, Kenneth M.; Kooyers, Nicholas J.; Johnson, Marc T. J.; Hodgins, Kathryn A.; Ness, Rob W.

doi:10.1093/gbe/evad146

Cited by 8 publications

(1 citation statement)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Sequences were processed using a common pipeline (https://github.com/James-S-Santangelo/glue_dnaSeqQC) and aligned to a chromosome-level genome assembly (56). For demographic analysis, we extracted 4-fold degenerate sites using the Degeneracy Pipeline (https://github.com/tvkent/Degeneracy) and utilized all sites for genome scans.…”

Section: Analysis Of Demography and Worldwide Population Structurementioning

confidence: 99%

Structural variants underlie parallel adaptation following global invasion

Battlay,

Hendrickson,

Mendez-Reneau

et al. 2024

Preprint

View full text Add to dashboard Cite

Rapid adaptation during invasion has historically been considered limited and unpredictable. We leverage whole-genome sequencing of >2600 plants across six continents to investigate the relative roles of colonization history and adaptation during the worldwide invasion of Trifolium repens. Introduced populations contain high levels of genetic variation with independent colonization histories evident on different continents. Five large structural variants on three chromosomes exist as standing genetic variation within the native range, and exhibit strong signatures of parallel climate-associated adaptation across continents. Common gardens in the native and introduced ranges demonstrate that three structural variants exhibit patterns of selection consistent with local adaptation across each range. Our results provide strong evidence that rapid and parallel adaptation during invasion is caused by large-effect structural variants introduced throughout the world.

show abstract

Section: Analysis Of Demography and Worldwide Population Structurementioning

confidence: 99%

Structural variants underlie parallel adaptation following global invasion

Battlay,

Hendrickson,

Mendez-Reneau

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

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

Plačková,

Bureš,

Lysak

et al. 2024

Annals of Botany

View full text Add to dashboard Cite

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

show abstract

Signatures of selective sweeps in urban and rural white clover populations

Santangelo,

Johnson,

Ness

2024

Preprint

View full text Add to dashboard Cite

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

show abstract

Haplotype-Resolved, Chromosome-Level Assembly of White Clover (Trifolium repens L., Fabaceae)

Cited by 8 publications

References 72 publications

Structural variants underlie parallel adaptation following global invasion

Structural variants underlie parallel adaptation following global invasion

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

Signatures of selective sweeps in urban and rural white clover populations

Contact Info

Product

Resources

About