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- Title
Improved contiguity of the threespine stickleback genome using long-read sequencing.
- Authors
Nath, Shivangi; Shaw, Daniel E.; White, Michael A.
- Abstract
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 76.7% of the gaps in the existing reference genome assembly, improving contiguity over fivefold. 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
- Subjects
THREESPINE stickleback; GENOMES; GENETIC models; FRESHWATER fishes; GENOMICS
- Publication
G3: Genes | Genomes | Genetics, 2021, Vol 11, Issue 2, p1
- ISSN
2160-1836
- Publication type
Article
- DOI
10.1093/g3journal/jkab007