Gasterosteus aculeatus gynogenetic reference genome and functional annotations version 1 and raw PacBio and Illumina data

Whole genome sequencing enables us to ask fundamental questions about the genetic basis of adaptation, population structure, and epigenetic mechanisms, but usually requires a suitable reference genome for making sense of the sequence data. While the availability of reference genomes has significantly improvement in both taxonomic coverage and overall quality, this poses a challenge for researchers in determining which reference genome best suits their data. Here we compare the use of two different reference genomes for the three-spined stickleback (Gasterosteus aculeatus), one novel genome from a European individual and the published reference genome of a North American individual. Specifically, we investigate the impact of using a local reference versus one generated from a differentiated population on several commonly used metrics in population genomics. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we confirmed genome quality is an ..., The induction of the diploid gynogen individual followed the protocol established for three-spined sticklebacks (Samonte-Padilla et al., 2011). In brief, fertilised stickleback eggs were mixed with UV-irradiated sperm (2 minutes of exposure) and then exposed to a heat-shock treatment of 34°C for 4 minutes, 5 minutes post-fertilisation. The treatment caused the genetic inactivation of the sperm, resulting in homozygote maternal offspring that lack paternal alleles (Samonte-Padilla et al., 2011). In order to increase the likelihood of embryo development, two siblings from the same family were used for this process. After 5 months post-hatching, a fish was sacrificed. DNA was extracted using the Qiagen high molecular weight extraction kit following the manufacturer’s protocol. Sequencing was then conducted at the Beijing Genomics Institute (BGI), taking place on a PacBio platform. In total, 2,805,993 reads were generated of which 214,285 were discarded before further analysis given their s...,