While the cost and time for assembling a genome has drastically decreased, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing technologies. Here, we use long-read sequencing to improve the contiguity of the threespine stickleback fish (Gasterosteus aculeatus) genome, a prominent genetic model species. Using Pacific Biosciences sequencing, we assembled a highly contiguous genome of a freshwater fish from Paxton Lake. Using contigs from this genome, we were able to fill over 76% of the gaps in the existing reference genome assembly, improving contiguity over five-fold. Our gap filling approach was highly accurate, validated by 10X Genomics long-distance linked-reads. In addition to closing a majority of gaps, we were able to assemble segments of telomeres and centromeres throughout the genome. This highlights the power of using long sequencing reads to assemble highly repetitive and difficult to assemble regions of genomes. This latest genome build has been released through a newly designed community genome browser that aims to consolidate the growing number of genomics datasets available for the threespine stickleback fish.

AbstractWhile the cost and time for assembling a genome have drastically reduced, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing technologies. Here, we use long sequencing reads to improve the contiguity of the threespine stickleback fish (Gasterosteus aculeatus) genome, a prominent genetic model species. Using Pacific Biosciences sequencing, we were able to fill over 76% of the gaps in the genome, improving contiguity over five-fold. Our approach was highly accurate, validated by 10X Genomics long-distance linked-reads. In addition to closing a majority of gaps, we were able to assemble segments of telomeres and centromeres throughout the genome. This highlights the power of using long sequencing reads to assemble highly repetitive and difficult to assemble regions of genomes. This latest genome build has been released through a newly designed community genome browser that aims to consolidate the growing number of genomics datasets available for the threespine stickleback fish.

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Allele-specific gene expression evolves rapidly across gametologs on heteromorphic sex chromosomes (X and Y or Z and W). Current models of sex chromosome evolution suggest this occurs through the rapid accumulation of mutations within regulatory regions. However, these patterns have not been demonstrated empirically due to the limited number of Y chromosome assemblies available to survey sequence evolution outside of coding regions. The threespine stickleback (Gasterosteus aculeatus) Y chromosome is an ideal model to test hypotheses of rapid regulatory evolution due to its intermediate state of divergence from the X chromosome. A large number of Y-linked gametologs still exist across three differently aged evolutionary strata to test these hypotheses. We found that putative enhancer regions (accessible chromatin regions defined through ATAC-seq) on the Y chromosome exhibited elevated substitution rates when compared to intergenic regions and synonymous sites within coding regions. This strongly suggests that many regulatory regions are under positive selection on the Y chromosome. This divergence was correlated with X-biased gametolog expression, indicating the loss of expression from the Y chromosome may be favored by selection. Our findings provide evidence that Y-linked regulatory regions exhibit signs of positive selection quickly after the suppression of recombination, supporting recent theoretical models that show the rapid divergence of regulatory regions may be favored to mask deleterious mutations on the Y chromosome.