Conservation genomics research often relies on accurate sex information to make inferences about species demography, dispersal, and population structure. However, field determined sex data are not always available and can be subject to human error, while laboratory sex assignment methods such as PCR assays can often be costly and challenging for non-model species. Conservation genomics programs increasingly use reduced-representation genome sequencing to assess neutral and functional genetic diversity, population structure, gene flow and pedigrees in threatened species. Here we demonstrate that sex can be determined from reduced-representation sequencing data produced by the increasingly popular Diversity Arrays Technology sequencing workflow (DArT-seq) using a program originally designed for application to shotgun data. This program—sexassign—compares the “dosage” of sequencing reads mapping to autosomes versus the X chromosome. In the present study, sexassign was used to identify the sex of 60 field-collected Greater Stick-Nest Rat (Leporillus conditor) samples, despite the absence of an annotated reference genome for the species. This “read-dosage” approach is not only more accurate and affordable than traditional sex assignment methods, but can be applied to any diploid organism with a heterogametic sex determination system—including non-model and understudied species of conservation importance—by using FASTQs generated by DArT.

保护基因组学研究通常依靠准确的性别信息来推断物种的人口统计学，分布和种群结构。但是，现场确定的性别数据并不总是可用，并且可能会受到人为错误的影响，而实验室性别分配方法（例如PCR分析）对于非模型物种而言往往是昂贵且具有挑战性的。保护基因组学计划越来越多地使用减少代表性的基因组测序来评估受威胁物种的中性和功能性遗传多样性，种群结构，基因流和谱系。在这里，我们证明，可以使用最初设计用于散弹枪数据的程序，根据日益流行的分集阵列技术测序工作流程（DArT-seq）产生的缩减表示形式的测序数据来确定性别。这个程序sexassign —比较映射到常染色体与X染色体的测序读段的“剂量”。在本研究中，尽管没有该物种的注释参考基因组，但仍使用sexassign来识别60个野外采集的大粘巢大鼠（Leporillus conditor）样品的性别。这种“读取剂量”方法不仅比传统的性别分配方法更准确，更实惠，而且可以通过使用生成的FASTQs，将其应用于具有异配子性别确定系统的任何二倍体生物体-包括对保护重要性无模型的和研究不足的物种由DArT。