The parasitic lifestyle of an archaeal symbiont

<strong>Abstract</strong> DPANN Archaea are a diverse group typically characterised by small cells and reduced genomes. To date, all cultivated DPANN Archaea<em> </em>are ectosymbionts that require direct cell contact with a host archaeal species for proliferation. However, the dynamics of DPANN – host interactions and the impacts of these interactions on host species are poorly understood. Here, we show that one DPANN archaeon (<em>Candidatus </em>Nanohaloarchaeum antarcticus) engages in parasitic interactions with its host (<em>Halorubrum lacusprofundi</em>) that result in host cell lysis. Our data also suggest that these interactions involve invasion of the host cell by the nanohaloarchaeon. This is the first reported instance of such a predatory-like lifestyle amongst Archaea and indicates that some DPANN Archaea<em> </em>may interact with host populations in a manner similar to viruses. If you find content useful and use part it for your work please cite this study. <strong>Repository contents</strong> <strong>1_Phylogenies.tar.gz</strong> includes all files needed to generate the phylogeny shown in Figure 4 of the associated manuscript. Specifically, this includes: The Workflow used to generated the species tree Any required dependencies such as custom scripts or custom databases The protein files from The proteins from all archaeal reference genomes that were used to generate the protein tree The 51 marker proteins used to generate the species tree The mafft_linsi alignments of the 51 marker proteins The BMGE trimmed alignments of the 51 marker proteins The concatenated alignment used to generate the species tree The output of the IQ-TREE analysis <strong>2_Protein_search.tar.gz</strong> includes all files needed to generate (a) the HMM profiles specific the two proteins with a coiled-coil protein (CCP) domain (referred to as Locus1 and Locus2 throughout the description) and (b) the Phyre2 results for all potential Locus1 and Locus2 proteins found in the archaea reference set. Specifically, this includes: (a) The script used to build the HMM profiles Any required dependencies The sequences of Locus1 and Locus2 proteins, including the individual proteins, the aligned proteins and the trimmed alignments. All HHsearch results The HMM profiles (b) The results for the batch search run for all potential Locus 1 and Locus2 proteins found across DPANN archaea The results for the sensitive search run for the Locus1 and Locus2 proteins from <em>Cand</em>. N. antarcticus <strong>3_Orthogroup_Data.tar.gz </strong>includes all files relating to groups of orthologous proteins generated by OrthoFinder. Specifically this includes: List of assemblies included in the analysis List of the number of proteins belonging to each orthogroup for each genome in the analysis. List of each orthogroup and the identifiers for each protein in each genome that were assigned to that orthogroup. List of the protein IDs for every protein in each orthogroup. Does not contain genome information. List of how many orthogroups are shared between each genome List of genes from each genome not assigned to an orthogroup Distribution of orthogroups across major phyla. General statistics for the orthogroups General statistic for each genome <strong>4_Pili_Phylogenies.tar.gz </strong>includes all files relating to generating single genes trees for pili-related genes (archaea-only and archaea and bacterial single protein trees). Includes: A list of investigated Pili genes Separately, for the archaeal-only and archaeal + bacterial species trees the: raw protein files, alignments, trimmed alignments, tree files**摘要** DPANN古菌是一类兼具多样性的类群，通常以细胞体积小巧、基因组简化为典型特征。截至目前，所有已分离培养的DPANN古菌均为外共生体，其增殖过程需要与宿主古菌物种建立直接细胞接触。然而，学界对于DPANN古菌与宿主的互作动态，以及这类互作对宿主物种的具体影响仍知之甚少。本研究发现，一种DPANN古菌——南极候选纳米盐古菌（*Candidatus Nanohaloarchaeum antarcticus*），可与其宿主深湖盐红菌（*Halorubrum lacusprofundi*）形成寄生互作，最终导致宿主细胞裂解。我们的研究数据还表明，这类互作涉及该纳米盐古菌对宿主细胞的入侵。这是学界首次在古菌域中报道此类类似捕食者的生活方式，同时表明部分DPANN古菌可通过类似病毒的方式与宿主种群产生互作。若您认为本研究内容具有参考价值并在工作中引用部分内容，请引用本研究。 **数据集内容** **1_系统发育分析文件.tar.gz** 包含生成相关论文图4所示系统发育树所需的全部文件，具体包括：用于构建物种树的分析流程、所需的自定义脚本或自定义数据库等依赖项、用于构建蛋白树的所有古菌参考基因组的蛋白序列文件、用于构建物种树的51个标记蛋白序列、51个标记蛋白的mafft_linsi比对结果、经BMGE修剪后的51个标记蛋白比对结果、用于构建物种树的拼接比对序列、IQ-TREE分析的输出结果。 **2_蛋白检索分析文件.tar.gz** 包含用于生成两类分析结果的全部所需文件：(a) 针对两个含有卷曲螺旋蛋白（coiled-coil protein, CCP）结构域的蛋白（本描述中记为基因座1和基因座2）的隐马尔可夫模型（Hidden Markov Model, HMM）特征文件；(b) 古菌参考数据集内所有潜在基因座1和基因座2蛋白的Phyre2分析结果。具体包括： (a) 用于构建HMM特征文件的脚本、所需依赖项、基因座1和基因座2的蛋白序列（包含单条蛋白序列、比对后的蛋白序列以及修剪后的比对序列）、所有HHsearch分析结果、HMM特征文件； (b) 针对DPANN古菌中所有潜在基因座1和基因座2蛋白的批量检索结果、南极候选纳米盐古菌（*Candidatus Nanohaloarchaeum antarcticus*）基因座1和基因座2蛋白的敏感检索结果。 **3_同源蛋白组数据文件.tar.gz** 包含所有由OrthoFinder生成的同源蛋白组相关文件，具体包括：本次分析纳入的组装序列列表、每个基因组中隶属于各同源蛋白组的蛋白数量列表、每个同源蛋白组及其对应基因组中被分配至该组的所有蛋白标识符列表、每个同源蛋白组内所有蛋白的ID列表（不包含基因组信息）、每两个基因组之间共享的同源蛋白组数量列表、每个基因组中未被分配至任何同源蛋白组的基因列表、主要古菌门之间的同源蛋白组分布情况、同源蛋白组的整体统计信息、各基因组的单独统计信息。 **4_菌毛相关系统发育分析文件.tar.gz** 包含所有用于构建菌毛相关基因单基因树的文件（分为仅古菌类群以及古菌与细菌类群的单蛋白树两类），具体包括：已研究的菌毛基因列表；针对仅古菌类群和古菌+细菌类群的物种树，分别提供原始蛋白序列文件、比对文件、修剪后的比对文件以及树文件。