Genomic Variation and Population Structure of the Threatened Neosho Madtom (Noturus placidus)

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. Lack of a reference genome necessitated variants be discovered using De Bruijn graphs implemented in CORTEX v1.0.5.21. Approximately 1.64 million high confidence single nucleotide polymorphisms (SNPs) were observed. Only 86,155 SNPs were variable across Neosho madtoms sequenced, indicating overall low level genetic diversity. While principal component analysis based on these genotypes accurately clustered individuals from the same location together, insignificant eigenvalues indicated weak population structure, suggesting these subpopulations are genetically compatible for reintroduction among these three locations. We also completed a draft de novo assembly of the Neosho madtom genome from 120X of sequences pooled across 3 individuals. We assembled the ~1 Gb genome into 149,885 contigs with a N50 of 12,261 bp, demonstrating 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 by sequencing mate pair libraries and to estimate historical effective population sizes.