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.

叶绿体序列数据被广泛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的可获得性不断提升，此前难以解决的古老分化事件迎来了厘清的契机。但另一方面，对大型多基因数据集进行恰当分析往往是一项重大挑战，因为这类数据常存在系统性偏差与冲突性信号。本研究从绿藻目（Sphaeropleales）类群中新增了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。我们对包含56个基因的数据集开展系统发育分析后发现，基于核苷酸水平进行分析可得到支持度优异的系统发育树，但该结果与对应的氨基酸水平分析结果存在显著差异。我们通过多组修改后的数据集分析，为该结果冲突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分进行了特征描述，进一步丰富了学界对叶绿体基因组演化的认知。