Department of Entomology, University of Georgia.
Genome Biol Evol. 2018 Mar 1;10(3):786-802. doi: 10.1093/gbe/evy036.
Many insects host facultative, bacterial symbionts that confer conditional fitness benefits to their hosts. Hamiltonella defensa is a common facultative symbiont of aphids that provides protection against parasitoid wasps. Protection levels vary among strains of H. defensa that are also differentially infected by bacteriophages named APSEs. However, little is known about trait variation among strains because only one isolate has been fully sequenced. Generating complete genomes for facultative symbionts is hindered by relatively large genome sizes but low abundances in hosts like aphids that are very small. Here, we took advantage of methods for culturing H. defensa outside of aphids to generate complete genomes and transcriptome data for four strains of H. defensa from the pea aphid Acyrthosiphon pisum. Chosen strains also spanned the breadth of the H. defensa phylogeny and differed in strength of protection conferred against parasitoids. Results indicated that strains shared most genes with roles in nutrient acquisition, metabolism, and essential housekeeping functions. In contrast, the inventory of mobile genetic elements varied substantially, which generated strain specific differences in gene content and genome architecture. In some cases, specific traits correlated with differences in protection against parasitoids, but in others high variation between strains obscured identification of traits with likely roles in defense. Transcriptome data generated continuous distributions to genome assemblies with some genes that were highly expressed and others that were not. Single molecule real-time sequencing further identified differences in DNA methylation patterns and restriction modification systems that provide defense against phage infection.
许多昆虫宿主兼性细菌共生体，这些共生体为宿主提供条件适应性益处。防御型汉森氏菌是蚜虫常见的兼性共生体，能为其提供对寄生蜂的保护。不同菌株的防御型汉森氏菌提供的保护水平不同，这些菌株也被不同的噬菌体（称为 APSE）感染。然而，由于仅对一个分离株进行了全序列测序，因此对菌株之间的特征变异知之甚少。由于相对较大的基因组大小以及在像蚜虫这样非常小的宿主中丰度较低，因此生成兼性共生体的完整基因组会受到阻碍。在这里，我们利用在蚜虫体外培养防御型汉森氏菌的方法，为豌豆蚜 Acyrthosiphon pisum 的 4 株防御型汉森氏菌生成了完整基因组和转录组数据。所选菌株也涵盖了防御型汉森氏菌的系统发育范围，并在抵御寄生蜂方面存在保护强度的差异。结果表明，菌株之间共享了大多数与营养获取、代谢和基本的细胞维护功能相关的基因。相比之下，移动遗传元件的库存差异很大，这导致了菌株在基因内容和基因组结构上的特异性差异。在某些情况下，特定的特征与抵御寄生蜂的差异相关，但在其他情况下，菌株之间的高变异性掩盖了与防御可能相关的特征的鉴定。转录组数据生成了与基因组组装相关的连续分布，其中一些基因高度表达，而另一些基因则不表达。单分子实时测序进一步确定了 DNA 甲基化模式和限制修饰系统的差异，这些差异为抵御噬菌体感染提供了保护。
