Abstract
BackgroundChlorophyceae is one of three most species-rich green algal classes and also the only class in core Chlorophyta whose monophyly remains uncontested as gene and taxon sampling improves. However, some key relationships within Chlorophyceae are less clear-cut and warrant further investigation. The present study combined genome-scale chloroplast data and rich sampling in an attempt to resolve the ordinal classification in Chlorophyceae. The traditional division into Sphaeropleales and Volvocales (SV), and a clade containing Oedogoniales, Chaetopeltidales, and Chaetophorales (OCC) was of particular interest with the addition of deeply branching members of these groups, as well as the placement of several incertae sedis taxa.MethodsWe sequenced 18 chloroplast genomes across Chlorophyceae to compile a data set of 58 protein-coding genes of a total of 68 chlorophycean taxa. We analyzed the concatenated nucleotide and amino acid datasets in the Bayesian and Maximum Likelihood frameworks, supplemented by analyses to examine potential discordant signal among genes. We also examined gene presence and absence data across Chlorophyceae.ResultsConcatenated analyses yielded at least two well-supported phylogenies: nucleotide data supported the traditional classification with the inclusion of the enigmatic Treubarinia into Sphaeropleales sensu lato. However, amino acid data yielded equally strong support for Sphaeropleaceae as sister to Volvocales, with the rest of the taxa traditionally classified in Sphaeropleales in a separate clade, and Treubarinia as sister to all of the above. Single-gene and other supplementary analyses indicated that the data have low phylogenetic signal at these critical nodes. Major clades were supported by genomic structural features such as gene losses and trans-spliced intron insertions in the plastome.DiscussionWhile the sequence and gene order data support the deep split between the SV and OCC lineages, multiple phylogenetic hypotheses are possible for Sphaeropleales s.l. Given this uncertainty as well as the higher-taxonomic disorder seen in other algal groups, dwelling on well-defined, strongly supported Linnaean orders is not currently practical in Chlorophyceae and a less formal clade system may be more useful in the foreseeable future. For example, we identify two strongly and unequivocally supported clades: Treubarinia and Scenedesminia, as well as other smaller groups that could serve a practical purpose as named clades. This system does not preclude future establishment of new orders, or emendment of the current ordinal classification if new data support such conclusions.
Highlights
Chlorophyta are a phylum of green plants comprising a variety of microscopic and macroscopic, uni- and multicellular, freshwater, terrestrial and marine algae that inhabit virtually every place on Earth that light and moisture can reach
The phylogenetic diversity of this phylum includes a number of deeply diverging lineages lumped under the term prasinophytes, and a group of core Chlorophyta, the majority of which falls into three classes (e.g., Fučíková et al, 2014a; Fučíková et al, 2014b)
For most of the 18 newly sequenced taxa, the full cp genome was not possible to assemble from the data, but full sequences of all or most protein-coding genes were recovered as were most of the rRNA and some of the tRNA genes
Summary
Chlorophyta are a phylum of green plants comprising a variety of microscopic and macroscopic, uni- and multicellular, freshwater, terrestrial and marine algae that inhabit virtually every place on Earth that light and moisture can reach. Within Chlorophyceae, two major sister clades are recognized –the SV and the OCC clade, composed of the orders Sphaeropleales and Volvocales (the latter is referred to as Chlamydomonadales in some sources), and Oedogoniales, Chaetophorales and Chaetopeltidales, respectively These five orders and the phylogenetic divide between SV and OCC are well accepted and supported by molecular phylogenies and ultrastructural features (Lewis et al, 1992; Turmel et al, 2008; Buchheim et al, 2012; Tippery et al, 2012; but compare to e.g., Pröschold et al, 2001, which does not show the SV split but yields no support for the alternative topology).
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