Faddeeva-Vakhrusheva Anna, Derks Martijn F L, Anvar Seyed Yahya, Agamennone Valeria, Suring Wouter, Smit Sandra, van Straalen Nico M, Roelofs Dick
Department of Ecological Science, Vrije University Amsterdam, Amsterdam, The Netherlands
Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
Genome Biol Evol. 2016 Jul 12;8(7):2106-17. doi: 10.1093/gbe/evw134.
Collembola (springtails) are detritivorous hexapods that inhabit the soil and its litter layer. The ecology of the springtail Orchesella cincta is extensively studied in the context of adaptation to anthropogenically disturbed areas. Here, we present a draft genome of an O. cincta reference strain with an estimated size of 286.8 Mbp, containing 20,249 genes. In total, 446 gene families are expanded and 1,169 gene families evolved specific to this lineage. Besides these gene families involved in general biological processes, we observe gene clusters participating in xenobiotic biotransformation. Furthermore, we identified 253 cases of horizontal gene transfer (HGT). Although the largest percentage of them originated from bacteria (37.5%), we observe an unusually high percentage (30.4%) of such genes of fungal origin. The majority of foreign genes are involved in carbohydrate metabolism and cellulose degradation. Moreover, some foreign genes (e.g., bacillopeptidases) expanded after HGT. We hypothesize that horizontally transferred genes could be advantageous for food processing in a soil environment that is full of decaying organic material. Finally, we identified several lineage-specific genes, expanded gene families, and horizontally transferred genes, associated with altered gene expression as a consequence of genetic adaptation to metal stress. This suggests that these genome features may be preadaptations allowing natural selection to act on. In conclusion, this genome study provides a solid foundation for further analysis of evolutionary mechanisms of adaptation to environmental stressors.
弹尾目昆虫（跳虫）是栖息于土壤及其枯枝落叶层的食腐六足动物。在适应人为干扰区域的背景下，对跳虫环纹奥氏跳虫的生态学进行了广泛研究。在此，我们展示了一个环纹奥氏跳虫参考菌株的基因组草图，估计大小为286.8兆碱基对，包含20249个基因。总共446个基因家族得到扩展，1169个基因家族是该谱系特有的。除了这些参与一般生物学过程的基因家族外，我们还观察到参与外源生物转化的基因簇。此外，我们鉴定出253例水平基因转移（HGT）。虽然其中最大比例的基因来自细菌（37.5%），但我们观察到此类真菌来源基因的比例异常高（30.4%）。大多数外源基因参与碳水化合物代谢和纤维素降解。此外，一些外源基因（如芽孢杆菌肽酶）在水平基因转移后得到扩展。我们推测，水平转移的基因可能有利于在充满腐烂有机物质的土壤环境中进行食物加工。最后，我们鉴定出几个谱系特异性基因、扩展基因家族以及水平转移基因，这些基因与因对金属胁迫的遗传适应导致的基因表达改变相关。这表明这些基因组特征可能是允许自然选择起作用的预适应。总之，这项基因组研究为进一步分析适应环境压力源的进化机制提供了坚实基础。
