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.

能够克隆繁殖的植物物种包括具有高度灭绝风险的稀有无菌物种，到影响生态系统结构的入侵植物。越来越多的证据表明，克隆性与繁殖力降低和分散能力有限会增加灭绝的风险。由于许多保护目标在基因上没有很好地表征，因此我们的目标是确定对减少的基因组表示进行测序的实用性，以告知非模式植物物种的保护。我们对来自最近描述的罕见克隆物种的单个DNA文库进行了测序。波斯菊。该库的多个程序集用于评估我们评估遗传变异和克隆分配，识别叶绿体单倍型并获得系统发育信息的能力。下一代测序（ddRADseq）提供了一种成本有效的方法，尽管与传统方法（例如微卫星）相比，丢失数据的水平有所提高，但仍可用于鉴定克隆和分配克隆体。我们应用遗传差异阈值来确定单个样品是否属于相同或不同的克隆。子发现该基因仅包含五个克隆，除一个位点外所有克隆均为单克隆-表明该物种的基因型多样性无法从茎的普查中确定。ddRADseq方法显示了系统发育分析的实用性，但我们使用来自同一文库的基因座鉴定了叶绿体单倍型分析的可能缺陷。