Department of Genetics, University of Georgia, Athens, GA 30602, USA.
G3 (Bethesda). 2021 Feb 9;11(2). doi: 10.1093/g3journal/jkab007.
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.
虽然组装基因组的成本和时间已经大大降低，但组装高度连续的基因组仍然是一个挑战。这些挑战正通过长读测序技术的整合迅速得到克服。在这里，我们使用长读测序来提高三刺鱼（Gasterosteus aculeatus）基因组的连续性，三刺鱼是一种重要的遗传模式物种。我们使用 Pacific Biosciences 测序，从 Paxton Lake 组装了一个高度连续的淡水鱼基因组。利用这个基因组的 contigs，我们能够填补现有参考基因组组装中超过 76.7%的缺口，连续性提高了五倍以上。我们的 gap filling 方法非常准确，通过 10X Genomics 长距离连锁reads 进行了验证。除了填补大部分缺口外，我们还能够组装整个基因组中的端粒和着丝粒片段。这突出了使用长测序reads 组装基因组中高度重复和难以组装区域的强大功能。这个最新的基因组构建已经通过一个新设计的社区基因组浏览器发布，该浏览器旨在整合越来越多的三刺鱼基因组学数据集。
