Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii

Abstract

Partial clonality, mode of reproduction, heterozygote excess, population genomics, kelp 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.

Population genomics ofPocilloporacorals: insights from RAD-sequencing

“…This is well visible in strictly asexual organisms such as the Euglenozoa Trypanosoma brucei gambiense (Weir et al, 2016). Despite the difficulty to delineate clonal lineages, RAD-Seq offers new avenue in the study of the reproduction of partially clonal organisms, such as in the Kelp Laminaria rodriguezii (Reynes et al, 2021). Several points in our results show the effect of clonality in the studied populations.…”

2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation

“…All three populations exhibited strongly negative F IS values based on the SNP genotyping, but the most clonal population (Faro) exhibited the lowest F IS (-0.51). Negative F IS has been shown to be strongly linked to the degree of clonality in facultative sexually reproducing species driven by genetic drift, both in theoretical ( Prugnolle and De Meeûs, 2008 ) and population genetic assessments ( Arnaud-Haond et al, 2020 ; Reynes et al, 2021b ). Moreover, F IS has been shown to be not as sampling-sensitive as genotypic richness (R) and has been suggested as the measure of choice for assessing the importance of clonal reproduction in seagrasses ( Arnaud-Haond et al, 2020 ).…”

Development of tools to rapidly identify cryptic species and characterize their genetic diversity in different European kelp species

“…In L. rodriguezii, Reynes et al 2021 demonstrated that SNPs markers were indeed highly efficient to investigate partial clonality under a population genomic approach, and identified a particularly high level of genetic differentiation in comparison to other kelps. Nevertheless, the use of SNPs from RRS is far more expensive compared to microsatellite genotyping and their study was restricted to a rather small number of individuals (N = 43).…”

“…This could be particularly interesting for L. pallida, which has not been investigated so far despite its ecological importance and biogeographical significance. For L. rodriguezii, genetic diversity within populations was until now only investigated using more than 4000 SNPs (Reynes et al 2021).…”

“…These technological advances in next-generation sequencing (NGS), are becoming available for studying population genetics in non-model organisms including kelps, such as reduced-representation sequencing (RRS) (Rad-seq SNPs: Guzinski et al 2018Guzinski et al , 2020Vranken et al 2021;Reynes et al, 2021) and whole genome sequencing (WGS, Graf et al 2021). In contrast with microsatellite loci that inform about patterns of genetic variation that result from neutral or stochastic processes; these new population genomic approaches characterized by a better covering of the genome allow to search for loci associated with coding regions and can be used to quantify adaptive variation, and inform about functional deterministic processes such as selection.…”