Table S3 from Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes.

Giant viruses have remarkable genomic repertoires—blurring the line with cellular life—and act as top–down controls of eukaryotic plankton. However, to date only six cultured giant virus genomes are available from the pelagic ocean. We used at-sea flow cytometry with staining and sorting designed to target wild predatory eukaryotes, followed by DNA sequencing and assembly, to recover novel giant viruses from the Pacific Ocean. We retrieved four ‘PacV’ partial genomes that range from 421 to 1605 Kb, with 13 contigs on average, including the largest marine viral genomic assembly reported to date. Phylogenetic analyses indicate that three of the new viruses span a clade with deep-branching members of giant Mimiviridae, incorporating the Cafeteria roenbergensis virus, the uncultivated terrestrial Faunusvirus, one PacV from a choanoflagellate and two PacV with unclear hosts. The fourth virus, oPacV-421, is phylogenetically related to viruses that infect haptophyte algae. About half the predicted proteins in each PacV have no matches in NCBI nr (e-value < 10−5), totalling 1735 previously unknown proteins; the closest affiliations of the other proteins were evenly distributed across eukaryotes, prokaryotes and viruses of eukaryotes. The PacVs encode many translational proteins and two encode eukaryotic-like proteins from the Rh family of the Ammonium transporter superfamily, likely influencing the uptake of nitrogen during infection. cPacV-1605 encodes a microbial viral rhodopsin (VirR) and the biosynthesis pathway for the required chromophore, the second finding of a choanoflagellate-associated virus that encodes these genes. In co-collected metatranscriptomes, 85% of cPacV-1605 genes were expressed, with capsids, heat shock proteins and proteases among the most highly expressed. Based on orthologue presence–absence patterns across the PacVs and other eukaryotic viruses, we posit the observed viral groupings are connected to host lifestyles as heterotrophs or phototrophs.This article is part of the discussion meeting issue ‘Single cell ecology’.

巨型病毒拥有极为丰富的基因组编码潜能，其与细胞生命的边界愈发模糊，同时也是真核浮游生物的下行调控因子。然而迄今为止，远洋海域中仅获取了6株可培养巨型病毒的基因组。
本研究采用针对野生捕食性真核生物设计的原位流式细胞术染色与分选流程，结合后续DNA测序与组装，从太平洋海域中获取了新型巨型病毒。我们共得到4个‘PacV’部分基因组，其长度介于421至1605千碱基对之间，平均包含13个重叠群（contig），其中包含迄今为止已报道的最大规模海洋病毒基因组组装序列。
系统发育分析显示，其中3株新型病毒与深层分支的巨型拟菌病毒科（Mimiviridae）成员构成一个演化支，这些成员包括 Cafeteria roenbergensis病毒、未培养的陆生Faunus病毒、1株分离自领鞭毛虫的PacV，以及另外2株宿主尚不明确的PacV。第4株病毒oPacV-421则与感染定鞭藻（haptophyte algae）的病毒具有系统发育相关性。
每株PacV中约有一半的预测蛋白质在NCBI非冗余蛋白质数据库（NCBI nr）中无匹配序列（e值<10^-5），总计得到1735种此前未被发现的蛋白质；其余蛋白质的最相近同源物则均匀分布于真核生物、原核生物以及真核生物病毒中。
PacV编码多种翻译相关蛋白质，其中2株还编码属于铵转运蛋白超家族Rh家族的类真核蛋白质，这可能会在感染过程中影响宿主对氮元素的摄取。cPacV-1605编码一种微生物病毒视紫红质（VirR）以及该蛋白所需生色团的生物合成通路，这是第二例被发现的携带此类基因的领鞭毛虫关联病毒。
在共采集得到的宏转录组数据中，cPacV-1605有85%的基因得到表达，其中衣壳蛋白、热休克蛋白以及蛋白酶的表达量位居前列。
基于PacV与其他真核病毒之间的直系同源基因存在/缺失模式，我们推测本次发现的病毒类群与其宿主的营养方式（异养或自养）存在关联。
本文属于‘单细胞生态学’专题讨论会议论文集的一部分。