Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida.
Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida.
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DOI：
10.1186/s12864-017-3852-x
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发表时间：
2017-06-28
期刊：
影响因子：
4.4
通讯作者：
Roelofs D
中科院分区：
文献类型：
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作者：
Faddeeva-Vakhrusheva A;Kraaijeveld K;Derks MFL;Anvar SY;Agamennone V;Suring W;Kampfraath AA;Ellers J;Le Ngoc G;van Gestel CAM;Mariën J;Smit S;van Straalen NM;Roelofs D
Folsomia candida 是土壤生物学的模型，属于 Isotomidae 科弹虫亚纲。它在沃尔巴克氏体存在的情况下进行孤雌生殖，并表现出显着的应激生理适应能力。为了更好地了解这些特征以及对土壤中生命的适应，我们在其孤雌生殖生活方式的背景下研究了它的基因组。我们应用 Pacific Bioscience 测序和组装生成了 221.7 Mbp 的念珠菌参考基因组，仅包含 162 个支架。其内共生体沃尔巴克氏体的完整基因组也被组装起来，并被证明是迄今为止发现的最大菌株。基因家族的大量扩展和谱系特异性基因簇与应激反应有关。通过水平基因转移获得了大量基因（809）。这些基因的很大一部分涉及木质纤维素降解。此外，还证实了涉及抗生素生物合成的基因的存在。观察到共线基因簇的基因组内重排，其中 11 个被组织为回文。与节肢动物共有簇相比，念珠菌的 Hox 基因簇显示出重大重排，导致簇杂乱无章。应激反应基因家族的扩展表明应激防御对于促进土壤定植很重要。大量与木质纤维素降解相关的 HGT 基因可能有利于释放土壤中的碳水化合物来源，特别是腐烂植物和真菌有机物中所含的碳水化合物来源。基因簇内和支架间的重复可能是其孤雌生殖生活方式的结果。这种高质量的基因组将有助于进化生物学家研究节肢动物的深层系统发育谱系，并将为更机械地理解土壤生态学和生态毒理学提供基础。本文的在线版本 (doi:10.1186/s12864-017-3852-x) 包含补充材料，可供授权用户使用。
Folsomia candida is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of Wolbachia, and exhibits remarkable physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the context of its parthenogenetic lifestyle. We applied Pacific Bioscience sequencing and assembly to generate a reference genome for F. candida of 221.7 Mbp, comprising only 162 scaffolds. The complete genome of its endosymbiont Wolbachia, was also assembled and turned out to be the largest strain identified so far. Substantial gene family expansions and lineage-specific gene clusters were linked to stress response. A large number of genes (809) were acquired by horizontal gene transfer. A substantial fraction of these genes are involved in lignocellulose degradation. Also, the presence of genes involved in antibiotic biosynthesis was confirmed. Intra-genomic rearrangements of collinear gene clusters were observed, of which 11 were organized as palindromes. The Hox gene cluster of F. candida showed major rearrangements compared to arthropod consensus cluster, resulting in a disorganized cluster. The expansion of stress response gene families suggests that stress defense was important to facilitate colonization of soils. The large number of HGT genes related to lignocellulose degradation could be beneficial to unlock carbohydrate sources in soil, especially those contained in decaying plant and fungal organic matter. Intra- as well as inter-scaffold duplications of gene clusters may be a consequence of its parthenogenetic lifestyle. This high quality genome will be instrumental for evolutionary biologists investigating deep phylogenetic lineages among arthropods and will provide the basis for a more mechanistic understanding in soil ecology and ecotoxicology. The online version of this article (doi:10.1186/s12864-017-3852-x) contains supplementary material, which is available to authorized users.