广泛分布的内共生菌Wolbachia的移动元件高度异质：Culex pipiens中候选二聚体质粒与高度片段化前噬菌体
Extensive mobilome heterogeneity in a widespread endosymbiont: A candidate dimeric plasmid and highly fragmented prophages in <i>Wolbachia</i> from <i>Culex pipiens</i>
研究团队用不依赖PCR扩增的Oxford Nanopore长读长测序策略，从单只解剖的雌性卵巢直接鉴定出Culex pipiens molestus中首个近完整的Wolbachia基因组及其移动元件。基于同一菌株个体的短读段数据验证了重复区候选突变。分析发现pWCP质粒存在新的二聚体结构，提示可能与活跃复制相关的多聚体质粒形式；前噬菌体WO区域即便在长读长下仍呈广泛片段化，原始长读段分析恢复出多种替代基因共线性，指向组装遗漏的异质前噬菌体结构。结果揭示了由整合型与游离型移动元件塑造的内共生菌基因组结构异质性。
来源：PLOS Genetics · journals.plos.org
by Alice Brunner, Maxime Mahout, Julien Amoros, Massilva Rahmoun, Mateo Jarry, Seth R. Bordenstein, Sarah R. Bordenstein, Blandine Trouche, Julie Reveillaud
The obligate, intracellular bacteria Wolbachia have gained increasing interest due to their selfish modifications of host arthropod reproduction, impacts on host evolution, and utility in vector control efforts to reduce arbovirus transmission worldwide. Despite their highly reduced genomes, Wolbachia harbor a rich mobilome that includes phages, insertion sequences and plasmids in mosquito vectors. However, these repeat-rich mobile genetic elements are notoriously difficult to assemble and can generate artificial, chimeric sequences that obscure their true diversity. As a result, conventional genome sequencing and assembly approaches often fail to resolve the complexity, leaving critical gaps of knowledge on how these elements evolve, mobilize, and shape both symbiont and host genomes. To address these challenges, we established a novel Oxford Nanopore long-read sequencing strategy that avoids prior PCR amplification and leverages single-dissected, female ovaries. Using this approach, we report and characterize—directly from native long-read molecules—the first near-complete Wolbachia genome and its mobile elements from individual ovaries of the mosquito vector Culex pipiens molestus. Additional short reads from individuals of the same strain were used to assess and validate candidate mutations, particularly in repetitive regions. We report a new dimeric structure of the pWCP plasmid, suggesting the existence of multimeric plasmid forms potentially associated with active replication. We also observed extensive fragmentation of prophage WO regions despite long read sequencing, underscoring their structural complexity. Raw long read analyses recovered multiple alternative gene syntenies within WO regions, pointing to heterogeneous prophage architectures missed by the assembly and marked diversity of WO elements in Wolbachia of Culex pipiens (wPip) group strains. Taken together, our results illuminate the structural heterogeneity of the endosymbiont genome that is shaped by integrated and episomal mobile elements.