Huang Xingyu, Yu Chen, Lu Longfei
Institute of Tibetan Plateau Research, Chinese Academy of Sciences, No. 16 Lincui Road, Chaoyang District, Beijing, 100101, People's Republic of China.
State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, People's Republic of China.
BMC Genomics. 2025 Mar 25;26(1):295. doi: 10.1186/s12864-025-11463-7.
Roseobacteraceae, often referred to as the marine roseobacter clade (MRC), are pivotal constituents of bacterial communities in coastal and pelagic marine environments. During the past two decades, 75 roseophages that infect various Roseobacteraceae lineages have been isolated. The N4-like roseophage clade, which encompasses 15 members, represents the largest clade among these roseophages. N4-like phages form a monophyletic group, classified as family Schitoviridae. And all N4-like roseophages form a unique clade within Schitoviridae and has been classified as the Rhodovirinae subfamily.
In this study, we isolated a novel roseophage, vB_DshP-R7L, that infects Dinoroseobacter shibae DFL12 from Xiamen Bay in the East China Sea. Conserved genes of Schitoviridae have been identified in the genome of vB_DshP-R7L, and following phylogenetic analysis suggests that the newly isolated phage is a member of the Rhodovirinae subfamily and represents the sole member of a novel genus, Gonggongvirus. The genome of vB_DshP-R7L harbors six auxiliary metabolic genes (AMGs), most of which potentially enhance DNA de novo synthesis. Additionally, a gene encoding ribosomal protein was identified. Comparative genomic analysis of AMG content among Rhodovirinae indicates a distinct evolutionary history characterized by independent ancient horizontal gene transfer events. Read-mapping analysis reveals the prevalence of vB_DshP-R7L and other Rhodovirinae roseophages in estuarine waters.
Our work illustrates the genomic features of a novel roseophage clade among the subfamily Rhodovirinae. The AMG content of vB_DshP-R7L is under severe purification selection, which reveals their possible ecological importance. We also demonstrated that vB_DshP-R7L and other Rhodovirinae roseophages are only detected in estuaries. Our isolation and characterization of this novel phage expands the understanding of the phylogeny, gene transfer history, and biogeography of Rhodovirinae infecting marine Roseobacteraceae.
红杆菌科（Roseobacteraceae），常被称为海洋红杆菌分支（MRC），是沿海和远洋海洋环境中细菌群落的关键组成部分。在过去二十年中，已分离出75种感染各种红杆菌科谱系的玫瑰噬菌体。包含15个成员的N4样玫瑰噬菌体分支是这些玫瑰噬菌体中最大的分支。N4样噬菌体形成一个单系群，被归类为裂病毒科（Schitoviridae）。所有N4样玫瑰噬菌体在裂病毒科中形成一个独特的分支，并被归类为红病毒亚科（Rhodovirinae）。
在本研究中，我们分离出一种新型玫瑰噬菌体vB_DshP-R7L，它感染来自中国东海厦门湾的希氏玫瑰杆菌（Dinoroseobacter shibae）DFL12。在vB_DshP-R7L的基因组中已鉴定出裂病毒科的保守基因，系统发育分析表明，新分离的噬菌体是红病毒亚科的成员，代表一个新属——共工病毒属（Gonggongvirus）的唯一成员。vB_DshP-R7L的基因组含有六个辅助代谢基因（AMG），其中大多数可能增强DNA从头合成。此外，还鉴定出一个编码核糖体蛋白的基因。对红病毒亚科中AMG含量的比较基因组分析表明，其具有以独立的古老水平基因转移事件为特征的独特进化历史。读段映射分析揭示了vB_DshP-R7L和其他红病毒亚科玫瑰噬菌体在河口水中的流行情况。
我们的工作阐明了红病毒亚科中一个新型玫瑰噬菌体分支的基因组特征。vB_DshP-R7L的AMG含量处于严格的纯化选择之下，这揭示了它们可能的生态重要性。我们还证明，vB_DshP-R7L和其他红病毒亚科玫瑰噬菌体仅在河口被检测到。我们对这种新型噬菌体的分离和表征扩展了对感染海洋红杆菌科的红病毒亚科的系统发育、基因转移历史和生物地理学的理解。
