Data from: Lack of genetic diversity across diverse immune genes in an endangered mammal, the Tasmanian devil (Sarcophilus harrisii)

The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction due to the spread of Devil Facial Tumour Disease. Polymorphisms in immune genes can provide adaptive potential to resist diseases. Previous studies in diversity at immune loci in wild species have almost exclusively focused on genes of the Major Histocompatibility Complex (MHC); however these genes only account for a fraction of immune gene diversity. Devils lack diversity at functionally important immunity loci, including MHC and Toll-like Receptor genes. Whether there are polymorphisms at devil immune genes outside these two families is unknown. Here, we identify polymorphisms in a wide range of key immune genes, and develop assays to type single nucleotide polymorphisms (SNPs) within a subset of these genes. A total of 167 immune genes were examined, including cytokines, chemokines and natural killer cell receptors. Using genome-level data from ten devils, SNPs within coding regions, introns and 10kb flanking genes of interest were identified. We found low polymorphism across 167 immune genes examined bioinformatically using whole-genome data. From this data, we developed long amplicon assays to target nine genes. These amplicons were sequenced in 29-220 devils and found to contain 78 SNPs, including eight SNPS within exons. Despite the extreme paucity of genetic diversity within these genes, signatures of balancing selection were exhibited by one chemokine gene, suggesting that remaining diversity may hold adaptive potential. The low functional diversity may leave devils highly vulnerable to infectious disease and therefore monitoring and preserving remaining diversity will be critical for the long-term management of this species. Examining genetic variation in diverse immune genes should be a priority for threatened wildlife species. This study can act as a model for broad-scale immunogenetic diversity analysis in threatened species.

袋獾（Sarcophilus harrisii）因袋獾面部肿瘤病的蔓延而濒临灭绝。免疫基因的多态性可为物种提供抗病适应潜力。以往针对野生物种免疫位点多样性的研究，几乎仅聚焦于主要组织相容性复合体（Major Histocompatibility Complex, MHC）基因，但这类基因仅占免疫基因多样性的一小部分。袋獾在包括MHC与Toll样受体（Toll-like Receptor）基因在内的功能关键免疫位点上缺乏遗传多样性，目前尚不明确这两类基因家族之外的袋獾免疫基因是否存在多态性。
本研究对一系列核心免疫基因开展了多态性鉴定，并开发了针对其中部分基因的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）分型检测方案。研究共检测167个免疫基因，涵盖细胞因子、趋化因子与自然杀伤细胞受体等类别。我们利用10只袋獾的全基因组数据，鉴定了目标基因编码区、内含子及基因侧翼10kb区域内的单核苷酸多态性。通过全基因组数据的生物信息学分析，发现167个免疫基因整体多态性水平偏低。
基于上述数据，我们开发了靶向9个基因的长扩增子检测方法。对29至220只袋獾的扩增子进行测序后，共检出78个单核苷酸多态性位点，其中8个位于外显子区域。尽管这些基因内的遗传多样性极度匮乏，但其中一个趋化因子基因呈现出平衡选择的特征，暗示残存的遗传多样性或具备适应潜力。较低的功能多样性可能使袋獾极易受传染病侵袭，因此监测并保护现存遗传多样性对该物种的长期保护管理至关重要。
针对多样化免疫基因的遗传变异开展研究，应成为濒危野生动物物种的优先工作方向。本研究可为濒危物种开展大规模免疫遗传多样性分析提供参考范式。