Biology

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Author: search.filters.author.Wilkinson, GeraldStart date: 2020

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    Transposable element annotation for a Genome Assembly of the stalk-eyed fly, Teleopsis dalmanni
    (2020-09-21) Wilkinson, Gerald; Baker, Richard; Reinhardt, Josephine
    Stalk-eyed flies in the genus Teleopsis carry selfish genetic elements that induce sex ratio meiotic drive (SR) and impact the fitness of male and female carriers. Here, we assemble and describe a chromosome-level genome assembly of the stalk-eyed fly, Teleopsis dalmanni, to elucidate patterns of divergence associated with SR. The genome contains tens of thousands of transposable element (TE) insertions and hundreds of transcriptionally and insertionally active TE families. By resequencing pools of SR and ST males using short and long-reads, we find widespread differentiation and divergence between XSR and XST associated with multiple nested inversions involving most of the sex ratio haplotype. Examination of genomic coverage and gene expression data revealed seven X-linked genes with elevated expression and coverage in SR males. The most extreme and likely drive candidate involves an XSR-specific expansion of an array of partial copies of JASPer, a gene necessary for maintenance of euchromatin and associated with regulation of TE expression. In addition, we find evidence for rapid protein evolution between XSR and XST for testis expressed and novel genes, i.e. either recent duplicates or lacking a dipteran ortholog, including an X-linked duplicate of maelstrom, which is also involved in TE silencing. Overall, the evidence suggests that this ancient XSR polymorphism has had a variety of impacts on repetitive DNA and its regulation in this species.
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    Gene Annotation for a Genome Assembly of the stalk-eyed fly, Teleopsis dalmanni
    (2020-09-14) Wilkinson, Gerald; Baker, Richard; Reinhardt, Josephine
    Stalk-eyed flies in the genus Teleopsis carry selfish genetic elements that induce sex ratio meiotic drive (SR) and impact the fitness of male and female carriers. Here, we assemble and describe a chromosome-level genome assembly of the stalk-eyed fly, Teleopsis dalmanni, to elucidate patterns of divergence associated with SR. The genome contains tens of thousands of transposable element (TE) insertions and hundreds of transcriptionally and insertionally active TE families. By resequencing pools of SR and ST males using short and long-reads, we find widespread differentiation and divergence between XSR and XST associated with multiple nested inversions involving most of the sex ratio haplotype. Examination of genomic coverage and gene expression data revealed seven X-linked genes with elevated expression and coverage in SR males. The most extreme and likely drive candidate involves an XSR-specific expansion of an array of partial copies of JASPer, a gene necessary for maintenance of euchromatin and associated with regulation of TE expression. In addition, we find evidence for rapid protein evolution between XSR and XST for testis expressed and novel genes, i.e. either recent duplicates or lacking a dipteran ortholog, including an X-linked duplicate of maelstrom, which is also involved in TE silencing. Overall, the evidence suggests that this ancient XSR polymorphism has had a variety of impacts on repetitive DNA and its regulation in this species.
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    Gene annotations for the Horvath37K_DNAMethylation array for 10 bat genomes
    (2020-09) Wilkinson, Gerald; Haghani, Amin; Horvath, Steve
    This submission contain gene annotations for an Illumina microarray (HorvathMammalMethylChip40) for 10 species of bats. The array design is available from the Gene Expression Omnibus (GEO) at NCBI as platform GPL28271. This array was used to generate DNA methylation data for nearly 700 known-aged individuals representing 26 species of bats. The resulting data were then used to predict age and species lifespan, and identify genomic regions that influence both of those traits.
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    Genotype data and linkage map for Teleopsis dalmanni, described in “Transposable element control disrupted by meiotic drive in a stalk-eyed fly genome
    (2020) Wilkinson, Gerald; Reinhardt, Josephine; Baker, Richard; Paczolt, Kimberly
    These files contain genotype matrices used to create a linkage map for the stalk-eyed fly, Teleopsis dalmanni. They were created from individuals derived from a backcross between two populations of flies derived from collections made in peninsular Malaysia and northern Sumatra. These linkage map was used to validate a chromosomal genome assembly, as described in a paper titled, “Transposable element control disrupted by meiotic drive in a stalk-eyed fly genome," which is being submitted for publication.