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 important factor in choosing a reference genome. A local
reference genome did offer increased mapping efficiency and genotyping
accuracy, likely stemming from the higher similarity in genome sequence
and synteny. Despite comparable distributions of the metrics generated
across the genome using SNP data (i.e., π, Tajima’s D, and FST),
window-based statistics using different references resulted in different
outlier genes and enriched gene functions. In contrast, the marker-based
analysis utilising DNA methylation distributions had a considerably higher
overlap in outlier genes and functions when using different reference
genomes. Overall, our results highlight how using a local reference genome
can increase the resolution of genome scans when multiple similar-quality
reference genomes are available. Such results have implications in the
detection of signatures of selection.