Data from: Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal Tree of Life.

Premise of the study: Phylogenomic analyses across the green algae are resolving relationships at the class, order and family levels, and highlighting dynamic patterns of evolution in organellar genomes. Here we present a within-family phylogenomic study to resolve genera and species relationships in the family Hydrodictyaceae (Chlorophyceae), for which poor resolution in previous phylogenetic studies, along with divergent morphological traits, have precluded taxonomic revisions.
Methods: Complete plastome sequences and mitochondrial protein-coding gene sequences were acquired from representatives of the Hydrodictyaceae using Next-Generation sequencing methods. Plastomes were characterized and gene order and content were compared with plastomes spanning the Sphaeropleales. Single-gene and concatenated-gene phylogenetic analyses of plastid and mitochondrial genes were performed.
Key results: The Hydrodictyaceae contain the largest sphaeroplealean plastomes thus far fully sequenced. Conservation of plastome gene order within Hydrodictyaceae is striking compared with more dynamic patterns revealed across Sphaeropleales. Phylogenetic analyses resolve Hydrodictyon sister to a monophyletic Pediastrum, though the morphologically distinct P. angulosum and P. duplex continue to be polyphyletic. Analyses of plastid data supported the neochloridacean genus Chlorotetraëdron as sister to Hydrodictyaceae, while conflicting signal was found in the mitochondrial data.
Conclusions: A phylogenomic approach resolved within-family relationships not obtainable with previous phylogenetic analyses. Denser taxon sampling across Sphaeropleales is necessary to capture patterns in plastome evolution, and further taxa and studies are needed to fully resolve sister lineage to Hydrodictyaceae and polyphyly of Pediastrum angulosum and P. duplex.

研究背景：绿藻的系统发育基因组学分析已可解析纲、目、科水平的亲缘关系，并揭示了细胞器基因组的动态演化模式。本研究针对隶属于绿藻纲（Chlorophyceae）的水网藻科（Hydrodictyaceae）开展科内系统发育基因组学研究，以厘清其属、种间的亲缘关系——此前的系统发育研究分辨率不足，加之形态性状存在分化，导致该类群无法进行分类修订。

研究方法：本研究利用下一代测序（Next-Generation sequencing）技术，从水网藻科代表类群中获取了完整的质体基因组（plastome）序列与线粒体蛋白编码基因序列。对获取的质体基因组进行注释分析，并与球藻目（Sphaeropleales）各分支的质体基因组比较基因排列顺序与基因组成。随后开展质体基因与线粒体基因的单基因及联合基因系统发育分析。

主要结果：水网藻科拥有目前已完成全测序的最大球藻目质体基因组。相较于球藻目整体呈现的动态演化模式，水网藻科内部的质体基因组基因排列保守性极强。系统发育分析显示，水网藻属（Hydrodictyon）与单系盘星藻属（Pediastrum）互为姊妹群，但形态特征显著分化的P. angulosum与P. duplex仍为多系类群。质体数据的分析结果支持新绿藻科（Neochloridaceae）的绿四胞藻属（Chlorotetraëdron）为水网藻科的姊妹谱系，而线粒体数据则呈现出冲突的系统发育信号。

研究结论：本研究采用系统发育基因组学方法，厘清了此前常规系统发育分析无法解析的科内亲缘关系。未来需扩大球藻目的类群采样范围，以充分解析质体基因组的演化模式；同时需补充更多类群与研究，以完全厘清水网藻科的姊妹谱系，以及P. angulosum和P. duplex的多系问题。