DOI: 10.5061/dryad.vmcvdncs9
title: Data from: Asexuality associated with marked genomic expansion of tandemly repeated rRNA and histone genes

description: 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
 and 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.
description: These data reflect a sequencing effort to compare genomic
 evolution (here, rDNA copy number specifically) in sexual vs. asexual
 lineages of the New Zealand freshwater snail, <em>Potamopyrgus
 antipodarum</em>. Illumina paired-end whole-genome sequnce data were
 generated from sexuals and asexuals collected from natural populations in
 New Zealand. In total, 16 lakes and 1 estuarary (the source for the
 outgroup used <em>P. estuarinus</em>) were sampled from. For
 sexual vs. asexual comparisons, 10 sexual and 16 asexual lineages were
 compared. Asexual <em>P. antipodarum</em> are polyploid,
 either triploid or tetraploid. The 16 asexuals included 11 triploids and 5
 tetraploid. An additional 12 triploid asexual samples were sequnced to
 examine copy number differences within and between clonal genotypes. These
 genotype-informed data represent 4 different clonal genotypes (3
 individuals sequenced/genotype; 2 genotypes from Lake Haupiri and 2
 genotypes from Lake Grasmer) determined by analyzing results from 46-SNP
 plate (same plate as used in Verhaegen et al. 2016) with GenoDive
 (Meirmans and Van Tienderen). See README
 and Supplemental_Tables_S1-S2.xlsx files for additional information about
 the processing. References: Meirmans PG, Van Tienderen PH.
 2004. GENOTYPE and GENODIVE: Two programs for the analysis of genetic
 diversity of asexual organisms. Mol. Ecol. Notes 4:792–794.
 Joshi NA, Fass JN. (2011). Sickle: A sliding-window, adaptive,
 quality-based trimming tool for FastQ files (Version 1.33). Available at
 https://github.com/najoshi/sickle Verhaegen G, McElroy KE, Bankers
 L, Neiman M, Haase M. (2018). Adaptive phenotypic plasticity in a clonal
 invader. Ecol. Evol. 8:4465–4483.