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Updated: Nov 17, 2025
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Microinjection for Transgenesis and Genome Editing in Threespine Sticklebacks
Published on: May 13, 2016
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Improved contiguity of the threespine stickleback genome using long-read sequencing.
Shivangi Nath1, Daniel E Shaw1, Michael A White1
1Department of Genetics, University of Georgia, Athens, GA 30602, USA.
G3 (Bethesda, Md.)
|February 18, 2021
Summary
Long-read sequencing dramatically improved the threespine stickleback fish genome assembly contiguity. This advancement aids in understanding this key genetic model species.
Area of Science:
- Genomics
- Comparative Genomics
- Bioinformatics
Background:
- Genome assembly remains challenging, particularly for achieving high contiguity.
- Long-read sequencing technologies are emerging as solutions for complex genome assembly.
Purpose of the Study:
- To enhance the contiguity of the threespine stickleback fish (Gasterosteus aculeatus) genome using long-read sequencing.
- To improve the existing reference genome assembly by filling gaps and assembling difficult regions.
Main Methods:
- Utilized Pacific Biosciences long-read sequencing for genome assembly.
- Employed contigs from the new assembly to fill gaps in the reference genome.
- Validated gap-filling accuracy using 10X Genomics linked-reads.
Main Results:
- Achieved a highly contiguous genome assembly for the threespine stickleback fish.
- Filled over 76.7% of gaps in the existing reference genome, improving contiguity more than fivefold.
- Successfully assembled segments of telomeres and centromeres, including highly repetitive regions.
Conclusions:
- Long-read sequencing is powerful for assembling contiguous genomes, especially challenging repetitive regions.
- The improved genome assembly and new community browser will benefit threespine stickleback research.
- This work advances genomic resources for a prominent model organism.
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