The White Sands pupfish (Cyprinodon tularosa), endemic to New Mexico in Southwestern North America, is of conservation concern due in part to invasive species, chemical pollution, and groundwater withdrawal. Herein, we developed a draft reference genome and use it to provide biological insights into the evolution and conservation of C. tularosa. We used our assembly to localize microsatellite markers previously used to demarcate evolutionary significant units (ESU), quantified genomic divergence and transposable element profiles between species, and compared C. tularosa genomic diversity related species. Our de novo assembly of PacBio Sequel II error-corrected reads resulted in a 1.08 Gb draft genome with a contig N50 of 1.4 Mb and 25,260 annotated protein coding genes, including 95% of the expected Actinopterygii conserved complete single-copy orthologues. Many of the C. tularosa microsatellite markers used for conservation assessments fell within, or near, genes and exhibited a pattern of increased heterozygosity near genic areas compared to those in intergenic regions. Nuclear alignments between these two species revealed 193 genes contained in rapidly diverging tracts; transposable element profiles were largely concordant and suggest a shared, rapid expansion of LINE and Gypsy elements. Genome-wide heterozygosity was markedly lower in C. tularosa compared to estimates from other related species, probably because of smaller long-term effective population sizes constrained by their isolated and limited habitat. Overall, these inferences provide new insights into C. tularosa that should help inform future management efforts.

中文翻译：

---

濒临灭绝的白沙鳉（Cyprinodon tularosa）基因组揭示了低多样性和异质分化模式

White Sands pupfish ( Cyprinodon tularosa ) 是北美西南部新墨西哥州的特有种，部分由于入侵物种、化学污染和地下水抽取而受到保护。在此，我们开发了一份参考基因组草案，并使用它来提供对C进化和保护的生物学见解。图拉罗萨。我们使用我们的组装来定位以前用于划分进化显着单位 (ESU)、量化基因组差异和物种之间的转座因子谱的微卫星标记，并比较C。图拉罗萨基因组多样性相关物种。我们对 PacBio Sequel II 错误校正读数的从头组装产生了一个 1.08 Gb 的基因组草图，其中包含 1.4 Mb 的重叠群 N50 和 25,260 个带注释的蛋白质编码基因，包括 95% 的预期放线菌保守的完整单拷贝直向同源物。许多的Ç。用于保护评估的tularosa微卫星标记落在基因内或基因附近，并且与基因间区域相比，在基因区域附近表现出杂合性增加的模式。这两个物种之间的核比对揭示了 193 个基因包含在快速分化的区域中；转座因子谱在很大程度上是一致的，表明 LINE 和 Gypsy 元素共享、快速扩展。全基因组杂合度显着降低Ç。tularosa与其他相关物种的估计值相比，可能是因为其孤立和有限的栖息地限制了较小的长期有效种群规模。总的来说，这些推论为C提供了新的见解。tularosa应该有助于为未来的管理工作提供信息。