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Individual high-quality reads (dd-RADsequencing) from: Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii

Citation

Reynes, Lauric; Aurelle, Didier (2021), Individual high-quality reads (dd-RADsequencing) from: Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii, Dryad, Dataset, https://doi.org/10.5061/dryad.hmgqnk9dq

Abstract

The development of population genomic approaches in non-model species allows for renewed studies of the impact of reproductive systems and genetic drift on population diversity. Here, we investigate the genomic signatures of partial clonality in the deep water kelp Laminaria rodriguezii, known to reproduce by both sexual and asexual means. We compared these results with the species Laminaria digitata, a closely related species that differs by different traits, in particular its reproductive mode (no clonal reproduction). We analysed genome-wide variation with dd-RAD sequencing using 4077 SNPs in L. rodriguezii and 7364 SNPs in L. digitata. As predicted for partially clonal populations, we show that the distribution of FIS within populations of L. rodriguezii is shifted toward negative values, with a high number of loci showing heterozygote excess. This finding is the opposite of what we observed within sexual populations of L. digitata, characterized by a generalized deficit in heterozygotes. Furthermore, we observed distinct distributions of FIS among populations of L. rodriguezii, which is congruent with the predictions of theoretical models for different levels of clonality and genetic drift. These findings highlight that the empirical distribution of FIS is a promising feature for the genomic study of asexuality in natural populations. Our results also show that the populations of L. rodriguezii analysed here are genetically differentiated and probably isolated. Our study provides a conceptual framework to investigate partial clonality on the basis of RAD-sequencing SNPs. These results could be obtained without any reference genome, and are therefore of interest for various non-model species.

Methods

Individual reads available in the repository come from two double-digest RAD-sequencing libraries (ddRAD-seq), achieved by multiplexing 49 individuals of Laminaria rodriguezii and 130 individuals of Laminaria digitata, including 2 and 5 technical replicates, respectively (see Sample_information.txt). Libraries were prepared according to Peterson et al., (2012) with the following restriction enzymes: PstI and HhaI and then sequenced with 150 bp paired-end reads on Illumina Hiseq 4000 (Génome Québec Innovation core, McGill Univ., Montréal, Canada).

The remaining reads (in the directory) were checked for quality using FastQC v.0.11.7, trimmed to 137 bp after the removal of adapters sequencing by Trimmomatic, then demultiplexed according to their barcodes using Stacks's process_radtags (Catchen et al., 2011).

Each individual is represented by forward and reverse read-pair (e.g. "Name".trim.R1.fq.gz and "Name".trim.R2.fq.gz).

Individual high-quality reads of Laminaria digitata are avaible at: http://www.ncbi.nlm.nih.gov/bioproject/720920.

Funding

MARFOR, Award: Biodiversa/0004/2015

European FEDER Fund, Award: 1166-39417

Clonix2D, Award: ANR-18-CE32-0001

MARFOR, Award: Biodiversa/0004/2015

European FEDER Fund, Award: 1166-39417

Clonix2D, Award: ANR-18-CE32-0001