Data from: Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates

Marine alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell genome sequences from seven individually isolated cells. Genes expected of heterotrophic eukaryotes were found, with interesting exceptions like presence of proteorhodopsin and vacuolar H+-pyrophosphatase. Phylogenetic analysis of concatenated SSU and LSU rRNA gene sequences provided strong support for the paraphyly of MALV lineages. Dinoflagellate viral nucleoproteins were found only in MALV groups that branched as sister to dinokaryotes. Our findings indicate that multiple independent origins of several characteristics early in dinoflagellate evolution, such as a parasitic life style, underlie the environmental diversity of MALVs, and suggest they have more varied trophic modes than previously thought.

海洋囊泡虫类（Marine alveolates, MALVs）是一类多样性丰富且分布广泛的早期分支甲藻，但目前对该类群的认知大多来自少数可培养物种——这类物种在自然样本中通常丰度极低——或是基于PCR扩增的环境SSU核糖体RNA（SSU rRNA）基因序列的多样性分析。为更全面地解析MALVs的基因组，我们从7株单独分离的单细胞中获取了单细胞基因组序列。研究中检测到了异养真核生物预期具备的全部核心基因，但也存在若干值得关注的例外：例如检出了蛋白视紫红质（proteorhodopsin）与液泡型H+焦磷酸酶（vacuolar H+-pyrophosphatase）。对拼接后的SSU与LSU核糖体RNA（LSU rRNA）基因序列进行系统发育分析，结果强有力地支持了MALVs类群演化支的并系性。甲藻病毒核蛋白仅在演化分支上作为甲核生物（dinokaryotes）姊妹群的MALVs类群中被检出。本研究结果表明，甲藻演化早期若干性状（如寄生生活方式）曾多次独立起源，这一特征构成了MALVs环境多样性的基础；同时研究也暗示，MALVs的营养模式比此前学界认知的更为多样。