Department of Entomology, College of Plant Protection, Nanjing Agricultural University.
Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
Genome Biol Evol. 2019 Feb 1;11(2):521-530. doi: 10.1093/gbe/evz013.
Sinella curviseta, among the most widespread springtails (Collembola) in Northern Hemisphere, has often been treated as a model organism in soil ecology and environmental toxicology. However, little information on its genetic knowledge severely hinders our understanding of its adaptations to the soil habitat. We present the largest genome assembly within Collembola using ∼44.86 Gb (118X) of single-molecule real-time Pacific Bioscience Sequel sequencing. The final assembly of 599 scaffolds was ∼381.46 Mb with a N50 length of 3.28 Mb, which captured 95.3% complete and 1.5% partial arthropod Benchmarking Universal Single-Copy Orthologs (n = 1066). Transcripts and circularized mitochondrial genome were also assembled. We predicted 23,943 protein-coding genes, of which 83.88% were supported by transcriptome-based evidence and 82.49% matched protein records in UniProt. In addition, we also identified 222,501 repeats and 881 noncoding RNAs. Phylogenetic reconstructions for Collembola support Tomoceridae sistered to the remaining Entomobryomorpha with the position of Symphypleona not fully resolved. Gene family evolution analyses identified 9,898 gene families, of which 156 experienced significant expansions or contractions. Our high-quality reference genome of S. curviseta provides the genetic basis for future investigations in evolutionary biology, soil ecology, and ecotoxicology.
狭跗小跳虫（Sinella curviseta）是北半球分布最广泛的跳虫（弹尾目）之一，常被作为土壤生态学和环境毒理学的模式生物。然而，有关其遗传知识的信息很少，严重阻碍了我们对其适应土壤生境的理解。我们使用单分子实时太平洋生物科学测序（SMRT）技术获得的约 44.86 Gb（118X）数据，生成了弹尾目最大的基因组组装。最终的组装结果由 599 个支架组成，大小约为 381.46 Mb，N50 长度为 3.28 Mb，捕获了 95.3%完整和 1.5%部分节肢动物基准通用单拷贝直系同源物（n=1066）。还组装了转录本和环状化的线粒体基因组。我们预测了 23943 个蛋白编码基因，其中 83.88%得到转录组证据的支持，82.49%与 UniProt 中的蛋白记录匹配。此外，还鉴定了 222501 个重复序列和 881 个非编码 RNA。弹尾目系统发育重建支持 Tomoceridae 与剩余的 Entomobryomorpha 姐妹群关系，而 Symphypleona 的位置尚未完全确定。基因家族进化分析确定了 9898 个基因家族，其中 156 个经历了显著的扩张或收缩。我们获得的狭跗小跳虫高质量参考基因组为进化生物学、土壤生态学和生态毒理学的未来研究提供了遗传基础。
