The freshwater water flea Daphnia magna NIES strain genome as a resource for CRISPR/Cas9 gene targeting: The glutathione S-transferase omega 2 gene
The freshwater water flea Daphnia magna NIES strain genome as a resource for CRISPR/Cas9 gene targeting: The glutathione S-transferase omega 2 gene
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DOI：
10.1016/j.aquatox.2021.106021
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发表时间：
2021-11-30
影响因子：
4.5
通讯作者：
Lee, Jae-Seong
中科院分区：
文献类型：
--
作者：
Byeon, Eunjin;Kim, Min-Sub;Lee, Jae-Seong
水蚤 Daphnia magna 是枝角类中的一种小型淡水浮游动物。在这项研究中，我们组装了 D. magna NIES 菌株的基因组，该菌株广泛用于基因打靶，但尚未有基因组报道。我们使用牛津纳米孔测序工具的长读长测序数据进行组装。使用 3,231 个遗传标记，D. magna NIES 菌株的基因组草图被构建为具有 483 个未锚定重叠群的 10 个连锁群 (LG)，其基因组大小为 173.47 Mb。基因组N50值为12.54 Mb，基准通用单拷贝直系同源值为98.8%。 D. magna NIES 基因组中的重复元件为 40.8%，高于其他水蚤属。在 D. magna NIES 基因组中，有 15,684 个基因进行了功能注释。为了评估用于 CRISPR/Cas9 基因靶向的 D. magna NIES 菌株的基因组，我们选择了谷胱甘肽 S-转移酶 omega 2 (GST-O2)，它是水生生物中砷生物转化的重要基因，并通过高效组成 (25.0%) 的突变株系来靶向它。此外，我们还测量了野生型和 GST-O2 靶向 D. magna NIES 菌株的突变体之间对砷的反应的活性氧和抗氧化酶活性。在本研究中，我们以GST-O2为例展示了D. magna NIES菌株的基因组，这将有助于通过CRISPR/Cas9技术构建缺失突变体。
The water flea Daphnia magna is a small freshwater planktonic animal in the Cladocera. In this study, we assembled the genome of the D. magna NIES strain, which is widely used for gene targeting but has no reported genome. We used the long-read sequenced data of the Oxford nanopore sequencing tool for assembly. Using 3,231 genetic markers, the draft genome of the D. magna NIES strain was built into ten linkage groups (LGs) with 483 unanchored contigs, comprising a genome size of 173.47 Mb. The N50 value of the genome was 12.54 Mb and the benchmarking universal single-copy ortholog value was 98.8%. Repeat elements in the D. magna NIES genome were 40.8%, which was larger than other Daphnia spp. In the D. magna NIES genome, 15,684 genes were functionally annotated. To assess the genome of the D. magna NIES strain for CRISPR/Cas9 gene targeting, we selected glutathione S-transferase omega 2 (GST-O2), which is an important gene for the biotransformation of arsenic in aquatic organisms, and targeted it with an efficient make-up (25.0%) of mutant lines. In addition, we measured reactive oxygen species and antioxidant enzymatic activity between wild type and a mutant of the GST-O2 targeted D. magna NIES strain in response to arsenic. In this study, we present the genome of the D. magna NIES strain using GST-O2 as an example of gene targeting, which will contribute to the construction of deletion mutants by CRISPR/Cas9 technology.