Data from: Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution

Chloroplast sequence data are widely used to infer phylogenies of plants and algae. With the increasing availability of complete chloroplast genome sequences, the opportunity arises to resolve ancient divergences that were heretofore problematic. On the flip side, properly analyzing large multi-gene data sets can be a major challenge, as these data may be riddled with systematic biases and conflicting signals. Our study contributes new data from nine complete and four fragmentary chloroplast genome sequences across the green algal order Sphaeropleales. Our phylogenetic analyses of a 56-gene data set show that analyzing these data on a nucleotide level yields a well-supported phylogeny – yet one that is quite different from a corresponding amino acid analysis. We offer some possible explanations for this conflict through a range of analyses of modified data sets. In addition, we characterize the newly sequenced genomes in terms of their structure and content, thereby further contributing to the knowledge of chloroplast genome evolution.

叶绿体序列数据（chloroplast sequence data）已被广泛应用于推断植物与藻类的系统发育关系。随着完整叶绿体基因组序列（complete chloroplast genome sequences）的获取日益普及，学界迎来了解决此前颇具挑战性的古老分化事件的契机。但另一方面，对大型多基因数据集（multi-gene data sets）进行规范分析往往是一项重大挑战，因为此类数据可能充斥着系统偏差与冲突信号。本研究新增了绿藻目（Sphaeropleales）下9条完整叶绿体基因组序列与4条片段化叶绿体基因组序列的数据。我们对56基因数据集（56-gene data set）开展的系统发育分析显示，在核苷酸水平上对该数据进行分析可得到支持度良好的系统发育树——但该结果与对应氨基酸水平分析得到的结果存在显著差异。我们通过多组修改后数据集的系列分析，为这一冲突现象提供了若干可能的解释。此外，我们还对新测序的基因组的结构与组成进行了特征描述，从而进一步拓展了学界对叶绿体基因组演化的认知。