Genetic variation, population structure, and genome assembly of the threatened Neosho madtom catfish

The Neosho madtom (Noturus placidus) is a small catfish, generally less than 3 inches in length, unique to the Neosho-Spring River system within the Arkansas River Basin. It was federally listed as threatened in 1990, largely due to habitat loss. As part of conservation efforts, we generated whole genome Illumina paired-end sequence data from ten Neosho madtom (average 39X coverage) originating from three geographically separated subpopulations to evaluate genetic diversity and population structure. One slender madtom (Noturus exilis) was also sequenced as an outgroup. Although over 1 million variants were found between Neosho and slender madtom, only 86,155 SNPs were variable across the Neosho madtoms sequenced, indicating overall low level genetic diversity. In addition, principal component analysis based on these genotypes indicated weak population structure, suggesting these subpopulations are genetically compatible for reintroduction among the locations. Using only 50X coverage of paired-end and mate pair data, we assembled the Neosho madtom genome into 68,147 scaffolds with a scaffold N50 of 120 kb, demonstrating the value in assembling a genome from a population that is closely related to a species of economic interest (i.e., channel catfish, Ictalurus punctatus) but has lower genetic diversity and is easier to assemble. Ongoing efforts aim to improve the assembly and develop demographic models and genomic resources to investigate the basic biology of why such a low-diversity species can subsist and to assist in future conservation efforts.