Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan.
Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, Sapporo, Hokkaido, Japan.
J Hum Genet. 2020 Jan;65(1):41-48. doi: 10.1038/s10038-019-0684-3. Epub 2019 Nov 14.
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 S13 株是一种棘阿米巴共生体的嗜肺军团菌；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，但从共生体 DNA 中分离宿主的基因组 DNA 通常具有挑战性。在本研究中，我们成功地使用 PacBio RS II 鉴定了新衣原体 S13 的双峰基因组结构，该结构得到了来自 MinION 的超长读支持。一种模式由 2,586,667 和 231,307 bp 的圆形序列组成；另一种是通过长同源区域整合的两种序列。它们编码了 2175 个蛋白编码区，其中一些暗示是通过水平基因转移获得的。它们在 Neochlamydia 属中特异性保守，并在基因组中形成一个簇，可能是通过基因组复制的倍增形成的。此外，值得注意的是，测序的 DNA 是在不从宿主中分离共生体 DNA 的情况下获得的。这是一种简单而通用的技术，有助于对自然界中不同的宿主和共生体进行特征分析。
