The endangered White Sands pupfish (Cyprinodon tularosa) genome reveals low diversity and heterogenous patterns of differentiation

Abstract 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.