Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae)

Background: The class Chlorophyceae (Chlorophyta) includes morphologically and ecologically diverse green algae. Most of the documented species belong to the clade formed by the Chlamydomonadales (also called Volvocales) and Sphaeropleales. Although studies based on the nuclear 18S rRNA gene or a few combined genes have shed light on the diversity and phylogenetic structure of the Chlamydomonadales, the positions of many of the monophyletic groups identified remain uncertain. Here, we used a chloroplast phylogenomic approach to delineate the relationships among these lineages. Results: To generate the analyzed amino acid and nucleotide data sets, we sequenced the chloroplast DNAs (cpDNAs) of 24 chlorophycean taxa; these included representatives from 16 of the 21 primary clades previously recognized in the Chlamydomonadales, two taxa from a coccoid lineage (Jenufa) that was suspected to be sister to the Golenkiniaceae, and two sphaeroplealeans. Using Bayesian and/or maximum likelihood in...背景：绿藻纲（Chlorophyceae）隶属于绿藻门（Chlorophyta），包含形态与生态多样性均极为丰富的绿藻类群。目前已记载的绝大多数物种均隶属于衣藻目（Chlamydomonadales，亦称团藻目Volvocales）与球囊藻目（Sphaeropleales）共同构成的演化支。尽管基于细胞核18S核糖体RNA基因或少量联合基因的研究已阐明衣藻目的多样性与系统发育结构，但已鉴定出的诸多单系群（monophyletic groups）的系统发育位置仍未明确。本研究采用叶绿体系统基因组学（chloroplast phylogenomic）方法，旨在厘清这些类群间的演化关系。结果：为构建本次分析所用的氨基酸与核苷酸数据集，我们对24个绿藻纲类群的叶绿体DNA（chloroplast DNAs, cpDNAs）进行了测序；这些类群涵盖了衣藻目中此前已界定的21个主要演化支中的16个类群代表、2个隶属于被推测为绿囊藻科（Golenkiniaceae）姊妹群的球形藻类谱系（Jenufa属）的类群，以及2个球囊藻目类群。我们采用贝叶斯法（Bayesian）和/或最大似然法（maximum likelihood）进行……