Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA.
School of Forestry and Wildlife Sciences, Auburn University, Auburn, USA.
Mol Ecol Resour. 2021 Oct;21(7):2520-2532. doi: 10.1111/1755-0998.13447. Epub 2021 Jul 1.
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.
白沙犬齿鱼（Cyprinodon tularosa），仅分布于美国西南部新墨西哥州，由于入侵物种、化学污染和地下水抽取等因素，其生存受到威胁。本研究构建了白沙犬齿鱼的参考基因组草图，并利用该基因组探讨了白沙犬齿鱼的进化和保护生物学。我们利用组装结果定位了先前用于界定进化显著单元（Evolutionary Significant Unit, ESU）的微卫星标记，量化了种间基因组分歧和转座元件特征，并比较了与白沙犬齿鱼基因组多样性相关的物种。我们利用 PacBio Sequel II 纠错 reads 进行从头组装，得到了一个 1.08Gb 的基因组草图，contig N50 为 1.4Mb，注释出 25260 个蛋白编码基因，包含了预期的硬骨鱼纲保守完整单拷贝直系同源基因的 95%。先前用于保护评估的许多白沙犬齿鱼微卫星标记位于基因内或附近，与基因间区域相比，这些标记在基因区域附近表现出更高的杂合性。这两个物种之间的核基因组比对显示，193 个基因包含在快速分化的区域；转座元件特征基本一致，提示 LINE 和 Gypsy 元件存在共同的快速扩张。与其他相关物种相比，白沙犬齿鱼的全基因组杂合度明显较低，这可能是由于其孤立和有限的栖息地导致长期有效种群规模较小所致。总的来说，这些推断为白沙犬齿鱼提供了新的见解，应该有助于指导未来的管理工作。
