Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
Phyzen Genomics Institute, Seongnam 13558, South Korea.
Comp Biochem Physiol Part D Genomics Proteomics. 2021 Mar;37:100787. doi: 10.1016/j.cbd.2020.100787. Epub 2021 Jan 4.
To assemble the genome of the marine water flea Diaphanosoma celebensis, a sentinel model for marine environmental monitoring, we constructed a high-quality genome using PromethION and HiSeq 2500 platforms. The total length of the assembled genome was 100.08 Mb, with N50 = 2.56 Mb (benchmarking universal single-copy orthologs, 96.9%) and consisted of 179 scaffolds. A total of 15,427 genes were annotated, and orthologous gene clusters in D. celebensis were analyzed and compared with those of the cladocerans Daphnia magna and Daphnia pulex. In addition, phase I, II, and III detoxification gene families of cytochrome P450s, glutathione S-transferases, and ATP-binding cassette were fully identified and revealed lineage-specific gene loss and/or expansion, suggesting that the evolution of detoxification gene families likely modulates fitness and susceptibility in response to environmental stressors. The study improves our understanding of the detoxification-related gene system and should contribute to future studies of molecular ecotoxicology in cladoceran species and their responses to emerging pollutants.
为了组装海洋水蚤 Diaphanosoma celebensis 的基因组，这是一种用于海洋环境监测的有价值的模式生物，我们使用 PromethION 和 HiSeq 2500 平台构建了高质量的基因组。组装基因组的总长度为 100.08Mb，N50=2.56Mb（基于通用单拷贝直系同源物进行基准测试，96.9%），由 179 个支架组成。总共注释了 15427 个基因，并分析了 D. celebensis 中的直系同源基因簇，并与桡足类动物 Daphnia magna 和 Daphnia pulex 进行了比较。此外，还全面鉴定了细胞色素 P450s、谷胱甘肽 S-转移酶和 ATP 结合盒的 I 期、II 期和 III 期解毒基因家族，并揭示了谱系特异性基因丢失和/或扩张，表明解毒基因家族的进化可能调节适应环境胁迫的适应性和敏感性。该研究提高了我们对解毒相关基因系统的理解，应该有助于未来对桡足类物种的分子生态毒理学及其对新兴污染物的反应的研究。
