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Dryad

Data from: Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes:Leuciscidae)

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Jul 10, 2023 version files 333.90 MB

Abstract

We used Nextera-tagmented reductively amplified DNA (nextRAD) sequencing data to discover SNPs in Rio Grande silvery minnow samples of known and unknown sex; and we produced two contig level genomes from Nanopore long-read sequencing. Raw NextRAD was aligned to each of the genomes. Subsequent SNP calling and filtering were repeated independently to obtain two datasets, one using the female genome as reference (female-referenced dataset) and another using the male genome (male-referenced dataset). The SNP calling identified 4.46 M raw variants in female-referenced dataset and of these 16,714 biallelic SNPs were retained after all filtering steps. For this set of SNPs, the average depth of coverage for the retained 64 females was 35.81 (ranging from 8.94 to 86.88) and 33.14 for the retained 53 males (ranging from 18.93 to 65.56). When using the male genome as reference we obtained 3.77 M raw variants and 17,920 biallelic SNPs. In this case the average depth of coverage for the same 64 females was 36.01 (ranging from 8.99 to 87.34) and for the same 53 males was 33.36 (ranging from 19.23 to 66.27).