Neochlamydia strain S13 is an amoebal symbiont of an Acanthamoeba sp. The symbiont confers resistance to Legionella pneumophila on its host; however, the molecular mechanism underlying this resistance is not completely understood. Genome analyses have been crucial for understanding the complicated host–symbiont relationship but segregating the host’s genome DNA from the symbiont’s DNA is often challenging. In this study, we successfully identified a bimodal genomic structure in Neochlamydia strain S13 using PacBio RS II supported by ultra-long reads derived from MinION. One mode consisted of circular sequences of 2,586,667 and 231,307 bp; the other was an integrated sequence of the two via long homologous regions. They encoded 2175 protein-coding regions, some of which were implied to be acquired via horizontal gene transfer. They were specifically conserved in the genus Neochlamydia and formed a cluster in the genome, presumably by multiplication through genome replication. Moreover, it was notable that the sequenced DNA was obtained without segregating the symbiont DNA from the host. This is an easy and versatile technique that facilitates the characterization of diverse hosts and symbionts in nature.

新衣原体菌株S13是棘孢菌属（Acanthamoeba sp。）的变形虫共生体。共生体在其宿主上赋予对肺炎军团菌的抗性。然而，这种抗性的分子机制尚不完全清楚。基因组分析对于理解复杂的宿主-共生体关系至关重要，但是将宿主的基因组DNA与共生体的DNA分离通常是具有挑战性的。在这项研究中，我们成功地确定了新衣原体的双峰基因组结构。使用PacBio RS II的S13菌株，并支持源自MinION的超长读取。一种模式由2,586,667和231,307 bp的循环序列组成；另一个是两个通过长同源区域的整合序列。他们编码了2175个蛋白质编码区，其中一些被暗示是通过水平基因转移获得的。它们在新衣原体属中特别保守，并在基因组中形成簇，大概是通过基因组复制而形成的。此外，值得注意的是，获得的测序DNA没有将共生体DNA与宿主分离。这是一种简单且通用的技术，可帮助表征自然界中的多种宿主和共生体。