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’.

马氏藻纲（Mamiellophyceae）的浮游光合生物包含尺寸小于2 μm的最小真核生物，它们全球分布且构成近岸海洋生态系统的基础。目前已从3个属——奥斯托小球藻属（Ostreococcus）、巴哈藻属（Bathycoccus）与微单胞藻属（Micromonas）——的先前分离得到的克隆培养菌株中，获取了8条完整注释的13~22 Mb基因组，这些基因组为探究分析从自然环境中分离的单细胞扩增基因组（Single Cell Amplified Genomes, SAGs）的应用范围与技术挑战提供了理想的研究资源。本研究组装了塔拉海洋科考航次（Tara Oceans expedition）中采集的12份SAGs数据，以获取其原位（in situ）生态学的生物学认知——这类认知可能在菌株分离培养过程中丢失。尽管组装得到的核基因组并不完整，但仍足够推断4株奥斯托小球藻属SAGs的交配型。线粒体与叶绿体序列系统性存在于数据中，其占细胞总DNA的比例不足3%，这表明SAGs可作为检测非靶标序列（如病毒粒子（virions）序列）的合适实验底物。在测序流程中过滤交叉污染后，对非马氏藻纲组装序列的分析发现了2种新型的1.6 kb与1.8 kb环状DNA病毒；同时特定细菌与卵菌（Oomycete）序列的存在，暗示这些生物可能与马氏藻目（Mamiellales）共存。本文属于‘单细胞生态学’专题讨论会议特刊的一部分。