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Bioinformatic methods used in McElroy et al. (2021). Asexuality associated with marked genomic expansion of tandemly repeated rRNA and histone genes. Molecular Biology and Evolution.

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Pant_rDNAhistones

Description of methods, including scripts, for comparing rRNA and histone gene copy number in sexual and asexual lineages of the freshwater New Zealand snail, Potamopyrgus antipodarum.

These methods are associated with the manuscript accepted at Molecular Biology and Evolution, "Asexuality associated with marked genomic expansion of tandemly repeated rRNA and histone genes". https://doi.org/10.1093/molbev/msab121

Abstract:

How does asexual reproduction influence genome evolution? While is it clear that genomic structural variation is common and important in natural populations, we know very little about how one of the most fundamental of eukaryotic traits - mode of genomic inheritance - influences genome structure. We address this question with the New Zealand freshwater snail Potamopyrgus antipodarum, which features multiple, separately derived obligately asexual lineages that coexist and compete with otherwise similar sexual lineages. We used whole-genome sequencing reads from a diverse set of sexual and asexual individuals to analyze genomic abundance of a critically important gene family, rDNA (the genes encoding rRNAs), that is notable for dynamic and variable copy number. Our genomic survey of rDNA in P. antipodarum revealed two striking results. First, the core histone and 5S rRNA genes occur between tandem copies of the 18S-5.8S-28S gene cluster, a unique architecture for these crucial gene families. Second, asexual P. antipodarum harbor dramatically more rDNA-histone copies than sexuals, which we validated through molecular cytogenetic analysis. The repeated expansion of this genomic region in asexual P. antipodarum lineages following distinct transitions to asexuality represents a dramatic genome structural change associated with asexual reproduction - with potential functional consequences related to the loss of sexual reproduction.

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Bioinformatic methods used in McElroy et al. (2021). Asexuality associated with marked genomic expansion of tandemly repeated rRNA and histone genes. Molecular Biology and Evolution.

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