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：全绿藻门的系统基因组学分析正在厘清纲、目、科阶元的系统发育关系，并揭示细胞器基因组的动态演化模式。本研究针对绿藻纲（Chlorophyceae）水网藻科（Hydrodictyaceae）开展科内系统基因组学研究，以厘清该类群内属、种间的系统发育关系——既往系统发育研究分辨率不足，加之形态性状差异显著，导致该科至今无法开展分类修订。
研究方法：本研究通过下一代测序（Next-Generation sequencing）技术，获取了水网藻科代表物种的完整质体基因组（plastome）序列与线粒体蛋白编码基因（mitochondrial protein-coding gene）序列。对质体基因组进行注释，并与球藻目（Sphaeropleales）各分支的质体基因组比较基因序列与基因排列顺序。分别对质体、线粒体蛋白编码基因开展单基因及串联基因的系统发育分析。
主要结果：水网藻科拥有目前已完成全测序的球藻目类群中最大的质体基因组。与球藻目整体呈现的动态基因排列模式相比，水网藻科内部的质体基因组基因顺序具有极高的保守性。系统发育分析显示，水网藻属（Hydrodictyon）与单系群（monophyletic）的盘星藻属（Pediastrum）互为姐妹群，但形态特征显著不同的P. angulosum与P. duplex仍属于多系群（polyphyletic）。质体数据的分析结果支持新绿藻科（Neochloridaceae）的Chlorotetraëdron属为水网藻科的姐妹群，但线粒体数据则呈现出冲突的系统发育信号。
研究结论：系统基因组学方法成功厘清了既往系统发育研究无法解析的科内系统发育关系。未来需扩大球藻目的类群采样范围，以全面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姐妹支系以及P. angulosum和P. duplex的多系性问题。