土壤生物Sinella curviseta （弹尾纲）基因组组装  

张峰*   丁银环   周青松   吴军   罗阿蓉*   朱朝东

Genome Biology and Evolution, evz013, https://doi.org/10.1093/gbe/evz013

发表时间：2019年1月21日

摘要

Sinella curviseta 是北半球最普遍的弹尾虫（弹尾纲），经常被视为土壤生态学和环境毒理学中的模式生物。 然而，关于其遗传知识的信息很少严重阻碍了我们理解其对土壤栖息地适应性。我们使用~44.86 Gb（118X）的单分子实时Pacific Bioscience Sequel测序，在Collembola中展示最大的基因组组装。 599个大片段最终组装为~381.46Mb，N50长度为3.28Mb，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（BUSCO）（n = 1066）。 我们还组装了转录组和环状线粒体基因组。 我们预测了23,943个蛋白质编码基因，其中83.88％ 有转录组证据支持，82.49％有UniProt 蛋白质记录匹配 。 此外，我们还鉴定了222,501个重复序列和881个非编码RNA。 重建弹尾纲系统发育支持Tomoceridae是Entomobryomorpha中其它类群的姐妹群，而Symphypleona的位置没有得到完全解析。 基因家族进化分析确定了9,898个基因家族，其中156个经历了显著扩张或收缩。 S. curviseta  的高质量参考基因组为未来研究进化生物学、土壤生态学和生态毒理学的提供了遗传基础。

关键词：PacBio测序 ，   Entomobryidae ，   比较基因组学 ，   系统发育学 ，   基因家族

ACCEPTED MANUSCRIPT

A high-quality draft genome assembly of Sinella curviseta, a soil model organism (Collembola) 

Feng Zhang Yinhuan Ding Qing-Song Zhou Jun Wu Arong Luo Chao-Dong Zhu

Genome Biology and Evolution, evz013, https://doi.org/10.1093/gbe/evz013

Published: 21 January 2019

Abstract

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 non-coding 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.

Keywords: PacBio sequencing, Entomobryidae, comparative genomics, phylogenomics, gene family

Acknowledgments

This work was supported by the Strategic Priority Research Program of the Chinese Academy of Science (XDB310304). F.Z. and Y.D. were also supported by the National Natural Science Foundation of China (31772491), and a grant from the Key Laboratory of the Zoological Systematics and Evolution of the Chinese Academy of Sciences (Y229YX5105). C.Z. acknowledges funding supports by the National Science Fund for Distinguished Young Scholars (31625024).