A core phylogeny of Dictyostelia derived from 47 functionally divergent proteins retrieved from five existing and six newly sequenced genomes. Genome Based Phylogeny

Dictyostelia are a group of organisms with colonial multicellularity that are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of 6 group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the intermediate groups. Since the position of these groups and other early diverging taxa is crucial for understanding evolution of multicellularity in Dictyostelia, we sequenced six representative genomes for these taxa. We retrieved orthologs of 47 housekeeping proteins from the novel and published genomes of Dictyostelia and unicellular Amoebozoa and inferred phylogenies from single and concatenated alignments. The multi-locus phylogenies robustly show that groups 1 and 2 are sister clades in branch I, with the group-intermediate taxon D.polycarpum positioned as outgroup to group 2. Branch II consists of group 4, nested in group 3, with the group-intermediate taxa Dictyostellium polycephalum and Polysphondylium violaceum positioned as outgroup to groups 3 and 4, respectively. The position of Acytostelium ellipticum implies that somatic cells were both lost and regained in group 2. We identified two proteins and 5 sets of two concatenated proteins that individually reproduce this phylogeny. These genes can be used alone or together for classification of additional Dictyostelid taxa by gene amplification.

网柄菌类（Dictyostelia）是一类具有集群多细胞性的生物，隶属于以单细胞为主的变形虫门（Amoebozoa）。早期基于小亚基核糖体DNA（SSU rDNA）数据构建的系统发育树将所有网柄菌类划分为4个主要类群，但未能明确其根部以及6个类群中间类群的系统发育位置。近期基于已测序基因组中的30或213个蛋白质构建的系统发育树，将根部定位于两个分支之间，每个分支各包含两个主要类群，但缺乏用于确定中间类群系统发育位置的数据。由于这些类群以及其他早期分化类群的系统发育位置对于理解网柄菌类的多细胞性演化至关重要，本研究对这些类群中的6个代表性基因组进行了测序。我们从本次新测序以及已公开的网柄菌类和单细胞变形虫门的基因组中，检索得到47个持家蛋白质（housekeeping proteins）的直系同源序列，并基于单序列比对和串联序列比对构建了系统发育树。多基因座系统发育树稳健地显示，类群1和类群2为分支I中的姊妹群，类群中间类群多果网柄菌（D. polycarpum）被定为类群2的外类群。分支II包含类群4，且类群4嵌套于类群3之中，类群中间类群多头网柄菌（Dictyostellium polycephalum）和紫聚孢黏菌（Polysphondylium violaceum）分别被定为类群3和类群4的外类群。椭胞无柄黏菌（Acytostelium ellipticum）的系统发育位置表明，类群2中曾发生体细胞的丢失与复得事件。本研究鉴定出2个蛋白质以及5组双蛋白质串联组合，其中每一组均可独立复现本次构建的系统发育树。这些基因可单独或联合使用，通过基因扩增技术对其他网柄菌类群进行分类鉴定。