Data from: Distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae Scherffelia dub and Tetraselmis sp. CCMP 881

The Chlorodendrophyceae is a small class of green algae belonging to the core Chlorophyta, an assemblage that also comprises the Pedinophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Here we describe for the first time the chloroplast genomes of chlorodendrophycean algae (Scherffelia dubia, 137,161 bp; Tetraselmis sp. CCMP 881, 100,264 bp). Characterized by a very small single-copy (SSC) region devoid of any gene and an unusually large inverted repeat (IR), the quadripartite structures of the Scherffelia and Tetraselmis genomes are unique among all core chlorophytes examined thus far. The lack of genes in the SSC region is offset by the rich and atypical gene complement of the IR, which includes genes from the SSC and large single-copy regions of prasinophyte and streptophyte chloroplast genomes having retained an ancestral quadripartite structure. Remarkably, seven of the atypical IR-encoded genes have also been observed in the IRs of pedinophycean and trebouxiophycean chloroplast genomes, suggesting that they were already present in the IR of the common ancestor of all core chlorophytes. Considering that the relationships among the main lineages of the core Chlorophyta are still unresolved, we evaluated the impact of including the Chlorodendrophyceae in chloroplast phylogenomic analyses. The trees we inferred using data sets of 79 and 108 genes from 71 chlorophytes indicate that the Chlorodendrophyceae is a deep-diverging lineage of the core Chlorophyta, although the placement of this class relative to the Pedinophyceae remains ambiguous. Interestingly, some of our phylogenomic trees together with our comparative analysis of gene order data support the monophyly of the Trebouxiophyceae, thus offering further evidence that the previously observed affiliation between the Chlorellales and Pedinophyceae is the result of systematic errors in phylogenetic reconstruction.绿枝藻纲（Chlorodendrophyceae）是一类小型绿藻，隶属于核心绿藻门（core Chlorophyta），该类群同时涵盖被孢藻纲（Pedinophyceae）、共球藻纲（Trebouxiophyceae）、石莼纲（Ulvophyceae）及绿藻纲（Chlorophyceae）。本研究首次报道了绿枝藻纲藻类的叶绿体基因组（chloroplast genome），分别为Scherffelia dubia（137161 bp）与四鞭藻属（Tetraselmis）未定种CCMP 881（100264 bp）。二者的叶绿体基因组均具备无任何基因编码的超小单拷贝（single-copy, SSC）区域，以及异常庞大的反向重复（inverted repeat, IR）区域；其四分体结构在迄今已研究的所有核心绿藻中独一无二。单拷贝区无基因编码的特征，由反向重复区丰富且非典型的基因组成所弥补：该反向重复区包含了保留祖先四分体结构的青绿藻（prasinophyte）与链形植物（streptophyte）叶绿体基因组中单拷贝区及大单拷贝区的基因。值得注意的是，其中7个非典型的反向重复区编码基因，也在被孢藻纲与共球藻纲的叶绿体基因组反向重复区中被发现，这表明这些基因极有可能早在所有核心绿藻的共同祖先的反向重复区中就已存在。鉴于核心绿藻主要谱系间的系统发育关系仍未明确，本研究评估了将绿枝藻纲纳入叶绿体系统基因组学分析的影响。我们采用来自71种绿藻的79个与108个基因数据集构建系统发育树，结果显示绿枝藻纲是核心绿藻的一个深分支谱系，不过该纲与被孢藻纲的系统发育位置关系仍存在歧义。有趣的是，部分系统基因组学树以及我们的基因排列顺序比较分析结果支持共球藻纲为单系群，这进一步佐证了此前观察到的小球藻目（Chlorellales）与被孢藻纲的亲缘关联，实则是系统发育重建过程中引入的系统误差所致。