Genbank accession numbers for virus sequences used in Fig.5. from Single Cell Ecogenomics reveals mating types of individual cells and ssDNA viral infections in the Smallest Photosynthetic Eukaryotes

Planktonic photosynthetic organisms of the class Mamiellophyceae include the smallest eukaryotes (less than 2 µm), are globally distributed and form the basis of coastal marine ecosystems. Eight complete fully annotated 13–22 Mb genomes from three genera, <i>Ostreococcus</i>, <i>Bathycoccus</i> and <i>Micromonas</i>, are available from previously isolated clonal cultured strains and provide an ideal resource to explore the scope and challenges of analysing Single Cell Amplified Genomes (SAGs) isolated from a natural environment. We assembled data from 12 SAGs sampled during the Tara Oceans expedition to gain biological insights about their <i>in situ</i> ecology, which might be lost by isolation and strain culture. Although the assembled nuclear genomes were incomplete, they were large enough to infer the mating types of four <i>Ostreococcus</i> SAGs. The systematic occurrence of sequences from the mitochondria and chloroplast, representing less than 3% of the total cell's DNA, intimates that SAGs provide suitable substrates for detection of non-target sequences, such as those of virions. Analysis of the non-Mamiellophyceae assemblies, following filtering out cross-contaminations during the sequencing process, revealed two novel 1.6 and 1.8 kb circular DNA viruses, and the presence of specific Bacterial and Oomycete sequences suggests that these organisms might co-occur with the Mamiellales.This article is part of the discussion meeting issue ‘Single cell ecology’.

玛米藻纲（Mamiellophyceae）的浮游光合生物包含体型最小的真核生物（直径小于2微米），它们在全球范围内广泛分布，是近岸海洋生态系统的基础类群。目前已有来自3个属——奥斯托藻属（Ostreococcus）、深海球藻属（Bathycoccus）与微球藻属（Micromonas）——的8条完整注释的13~22兆碱基对（Mb）全基因组，这些基因组均来自已分离的克隆培养菌株，为探究分析自然环境中分离的单细胞扩增基因组（Single Cell Amplified Genomes, SAGs）的研究范围与挑战提供了理想的研究资源。本研究对塔拉海洋科考（Tara Oceans）期间采集的12份SAGs数据进行组装，以期获取这些生物的原位（in situ）生态学信息——这类信息往往在分离与菌株培养过程中丢失。尽管组装得到的核基因组并不完整，但其规模已足以推断4份奥斯托藻属SAGs的交配型。线粒体与叶绿体序列系统性存在于组装数据中，占细胞总DNA的比例不足3%，这表明SAGs可作为检测非目标序列（如病毒粒子（virions）序列）的合适底物。在过滤掉测序过程中的交叉污染后，对非玛米藻纲组装序列的分析发现了2种新型环状DNA病毒，基因组长度分别为1.6和1.8千碱基对（kb）；同时检测到特异性的细菌（Bacterial）与卵菌（Oomycete）序列，提示这些类群可能与玛米藻目（Mamiellales）生物共存。本文属于“单细胞生态学”专题讨论会议论文集的一部分。