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.

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, Potamopyrgus antipodarum. 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 P. estuarinus) were sampled from. For sexual vs. asexual comparisons, 10 sexual and 16 asexual lineages were compared. Asexual P. antipodarum 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.