Biology subjects

Bracewell, R.

Publications and source records attributed to Bracewell, R..

6 recordsLinked to original sources

bioRxiv2025

Molecular Insights into the Production of Extracellular Vesicles by Plants

Extracellular vesicles (EVs) produced by Arabidopsis are highly heterogeneous in protein content. Specific EV subpopulations have been proposed to participate in plant immunity, particularly during plant-fungal interaction. To understand the origins of plant EV heterogeneity, we used a proximity labeling approach to identify proteins and pathways involved in the secretion of distinct EV subpopulations. Proximity labeling, co-immunoprecipitation, and fluorescence microscopy in Nicotiana benthamiana all indicated a general role in EV secretion for EXO70 proteins (a subunit of the exocyst complex) and the immune-related protein RPM1-INTERACTING PROTEIN 4 (RIN4), while the ER-localized VAMP-ASSOCIATED PROTEIN 27(VAP27) was specifically associated with the EV marker protein TETRAPSANIN8 (TET8). Despite being secreted in separate EV populations, we found that TET8 and PENETRATION 1 (PEN1) co-localized in multivesicular body-like subcellular structures. Based on these results, we tested Arabidopsis mutants and identified several proteins involved in EV secretion, including members of the exo70 family, rin4, rabA2a, scd1 (a GTP-exchange factor for RabE GTPases), and vap27. We also uncovered a possible connection between trichomes and EVs, as the trichomeless mutant glabrous1 secreted approximately half the number of EVs as wild type. Furthermore, PEN1 MVB-like structures were prevalent in guard cells, suggesting that guard cells may contribute to secretion of PEN1+ EVs on the leaf surface. Lastly, we found that exo70 family mutants are more susceptible to infection with the fungal pathogen Colletotrichum higginsianum, underlining the importance of secretion for plant immunity. Together, our results unravel some of the complex mechanisms that give rise to EV subpopulations in plants.

plant biology↗

bioRxiv2025

QTL identification and characterization of the recombination landscape of the mountain pine beetle (Dendroctonus ponderosae)

Insect pests can rapidly accumulate in number and thrive in diverse environments, making them valuable models for studying phenotypic plasticity and the genetic basis of local adaptation. The mountain pine beetle (Dendroctonus ponderosae) is a major forest pest and adult body size and generation time are two traits that vary among populations and directly influence reproductive success and outbreak dynamics. To identify regions of the genome linked to these two traits, we generated ddRAD sequencing data from an F2 intercross, using populations from two Y haplogroups with phenotypic and genetic differences in these traits. A high-density linkage map was generated and QTL analyses performed. We identified a single large effect QTL for generation time, associated with an adult diapause. The QTL spans the entire X chromosome, peaking over the evolutionarily conserved portion of the X. We were unable to detect a significant QTL for body size. Our linkage map identified putative inversions shared by parents that are absent in the published reference genome, with three putative inversions on chromosomes 2, 3, and the X. We also detected extensive regions of low recombination that were associated with low gene density, indicative of large pericentromeric regions. Surprisingly, we found that in our cross, F2 males inherited X chromosomes with significantly fewer crossover events than F2 females. Our findings provide information about the recombination landscape, the sex-biased inheritance of recombined Xs, and the genomic location of a key trait in a major forest pest.

genetics↗

bioRxiv2023

Sex chromosome evolution in beetles

Beetles are the most species-rich group of animals and harbor diverse karyotypes. Most species have XY sex chromosomes, but X0 sex determination mechanisms are also common in some groups. We generated a whole-chromosome assembly of a beetle species with a neo-sex chromosome and utilize eleven additional beetle genomes, to reconstruct karyotype evolution across Coleoptera. We identify ancestral linkage groups, termed Stevens elements, that share a conserved set of genes across beetles. While the ancestral X chromosome is maintained across beetles, we find independent additions of autosomes to the ancestral sex chromosomes. These neo-sex chromosomes evolve the stereotypical properties of sex chromosomes, including the evolution of dosage compensation, and a non-random distribution of genes with sex-biased expression. Beetles thus provide a novel model to gain a better understanding of the diverse forces driving sex chromosome evolution.

evolutionary biology↗

bioRxiv2019

Complex evolutionary history of the Y chromosome in flies of the Drosophila obscura species group

The Drosophila obscura species group shows dramatic variation in karyotype, including transitions among sex chromosomes. Members of the affinis and pseudoobscura subgroups contain a neo-X chromosome (a fusion of the X with an autosome), and it was shown that ancestral Y genes of Drosophila have become autosomal in species that contain the neo-X. Detailed analysis in species of the pseudoobscura subgroup revealed a translocation of ancestral Y genes to the small dot chromosome of that group. Here, we show that the Y-dot translocation is restricted to the pseudoobscura subgroup, and translocation of Y genes in the affinis subgroup followed a different route. We find that most ancestral Y genes moved independently to autosomal or X-linked locations in different taxa of the affinis subgroup, and we propose a dynamic model of sex chromosome formation and turnover in the obscura species group. Our results show that Y genes can find unique paths to escape an unfavorable genomic environment.

evolutionary biology↗

bioRxiv2019

Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome

The Drosophila obscura species group is one of the most studied clades of Drosophila and harbors multiple distinct karyotypes. Here we present a de novo genome assembly and annotation of D. bifasciata, a species which represents an important subgroup for which no high-quality chromosome-level genome assembly currently exists. We combined long-read sequencing (Nanopore) and Hi-C scaffolding to achieve a highly contiguous genome assembly approximately 193Mb in size, with repetitive elements constituting 30.1% of the total length. Drosophila bifasciata harbors four large metacentric chromosomes and the small dot, and our assembly contains each chromosome in a single scaffold, including the highly repetitive pericentromere, which were largely composed of Jockey and Gypsy transposable elements. We annotated a total of 12,821 protein-coding genes and comparisons of synteny with D. athabasca orthologs show that the large metacentric pericentromeric regions of multiple chromosomes are conserved between these species. Importantly, Muller A (X chromosome) was found to be metacentric in D. bifasciata and the pericentromeric region appears homologous to the pericentromeric region of the fused Muller A-AD (XL and XR) of pseudoobscura/affinis subgroup species. Our finding suggests a metacentric ancestral X fused to a telocentric Muller D and created the large neo-X (Muller A-AD) chromosome [~]15 MYA. We also confirm the fusion of Muller C and D in D. bifasciata and show that it likely involved a centromere-centromere fusion.

genomics↗

bioRxiv2019

Dynamic turnover of centromeres drives karyotype evolution in Drosophila

Centromeres are the basic unit for chromosome inheritance, but their evolutionary dynamics is poorly understood. We generate high-quality reference genomes for multiple Drosophila obscura group species to reconstruct karyotype evolution. All chromosomes in this lineage were ancestrally telocentric and the creation of metacentric chromosomes in some species was driven by de novo seeding of new centromeres at ancestrally gene-rich regions, independently of chromosomal rearrangements. The emergence of centromeres resulted in a drastic size increase due to repeat accumulation, and dozens of genes previously located in euchromatin are now embedded in pericentromeric heterochromatin. Metacentric chromosomes secondarily became telocentric in the pseudoobscura subgroup through centromere repositioning and a pericentric inversion. The former (peri)centric sequences left behind shrunk dramatically in size after their inactivation, yet contain remnants of their evolutionary past, including increased repeat-content and heterochromatic environment. Centromere movements are accompanied by rapid turnover of the major satellite DNA detected in (peri)centromeric regions.

evolutionary biology↗