Data from: Haploid gynogens facilitate disomic marker development in paleotetraploid sturgeons

Acipenseriformes (sturgeons and paddlefishes) are of substantial
conservation concern, and development of genomic resources for these
species is difficult due to past whole genome duplication. Development of
disomic markers for polyploid organisms can be challenging due to
difficulty in resolving alleles at a single locus from those among
duplicated loci. In this study, we detail the development of disomic
markers for the endangered pallid sturgeon (Scaphirhynchus albus) found in
North America. One of the strategies for pallid sturgeon conservation is
to stock U.S. rivers with offspring of pure pallid sturgeon, but
introgression with the sympatric shovelnose sturgeon (S. platorynchus)
threatens pallid sturgeon genetic integrity. Currently, 19 microsatellite
loci are used to differentiate between both species and their hybrids, but
the markers are insufficient to robustly identify backcrosses. We
performed double digest restriction site-associated DNA sequencing
(ddRADseq) on shovelnose sturgeon haploid gynogens to produce a
reduced-representation genomic reference. Contiguous sequences that were
heterozygous within a haploid individual were flagged as potentially
encompassing multiple loci. Approximately 60 individuals of each species
from two management units were sequenced, and reads were mapped to the
haploid reference to identify single nucleotide polymorphisms (SNPs) at
individual loci. The final dataset contained 11,082 microhaplotyped loci
which offer at least an order of magnitude greater resolution for species
discrimination than the current panel of 19 microsatellites. These markers
will be used to examine a larger sample of Scaphirhynchus individuals
throughout their ranges to determine the extent and trajectory of
hybridization.