Identification of clonemates and genetic lineages using next-generation sequencing (ddRADseq) guides conservation of a rare species, Bossiaea vombata (Fabaceae)

Abstract Plant species capable of clonal reproduction range from rare, sterile species that have a high extinction risk to invasive plants that influence the structure of ecosystems. There is increasing evidence that clonality in combination with reduced fecundity and limited dispersal capacity increases extinction risk. As many conservation targets are not well-characterised genetically, our objective was to determine the utility of sequencing a reduced representation of the genome to inform the conservation of a non-model plant species. We sequenced a single DNA library from a recently described, rare, clonal species; Bossiaea vombata. Multiple assemblies of that library were used to evaluate our ability to assess genetic variation and clonal assignment, to identify chloroplast haplotypes and to obtain phylogenetic information. Next generation sequencing (ddRADseq) provided a cost and time effective method for identifying clones and assigning clonemates despite increased levels of missing data in comparison to more traditional methods (e.g. microsatellites). We applied a threshold of genetic difference to determine whether individual samples belonged to the same or different clones. Bossiaea vombata, was found to comprise only five clones with all but one site being monoclonal - indicating that the genotypic diversity of the species cannot be determined from a census of stems. The ddRADseq method showed utility for phylogenetic analysis but we identified possible shortcomings in chloroplast haplotyping using loci from the same library.