Improved contiguity of the threespine stickleback genome using long-read sequencing

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.