ANALYSIS OF A PLASTID MULTIGENE DATA SET AND THE PHYLOGENETIC POSITION OF THE MARINE MACROALGA CAULERPA FILIFORMIS (CHLOROPHYTA)¹

Abstract

Molecular phylogenetic relationships within the Chlorophyta have relied heavily on rRNA data. These data have revolutionized our insight in green algal evolution, yet some class relationships have never been well resolved. A commonly used class within the Chlorophyta is the Ulvophyceae, although there is not much support for its monophyly. The relationships among the Ulvophyceae, Trebouxiophyceae, and Chlorophyceae are also contentious. In recent years, chloroplast genome data have shown their utility in resolving relationships between the main green algal clades, but such studies have never included marine macroalgae. We provide partial chloroplast genome data (∼30,000 bp, 23 genes) of the ulvophycean macroalga Caulerpa filiformis (Suhr) K. Herig. We show gene order conservation for some gene combinations and rearrangements in other regions compared to closely related taxa. Our data also revealed a pseudogene (ycf62) in Caulerpa species. Our phylogenetic results, based on analyses of a 23-gene alignment, suggest that neither Ulvophyceae nor Trebouxiophyceae are monophyletic, with Caulerpa being more closely related to the trebouxiophyte Chlorella than to Oltmannsiellopsis and Pseudendoclonium.

Phylogeny and Molecular Evolution of the Green Algae

“…Moreover, the monophyly of the class has been questioned because it lacks unique ultrastructural synapomorphies (Mattox & Stewart, 1984;O'Kelly & Floyd, 1984a). Several molecular phylogenetic studies provided weak or no support for monophyly of the Ulvophyceae and recovered two distinct lineages: the Oltmannsiellopsidales-Ulvales-Ulotrichales lineage and a clade consisting of Trentepohliales and the siphonocladous and siphonous seaweed orders (Zechman et al, 1990;Watanabe et al, 2001;López-Bautista & Chapman, 2003;Watanabe & Nakayama, 2007;Cocquyt et al, 2009;Zuccarello et al, 2009). More recently, a 10-gene phylogenetic analysis recovered the class as a well supported monophyletic group, and confirmed the divergence of two main ulvophycean clades (Cocquyt et al, 2010b).…”

“…18S analyses placed this genus within the Trebouxiophyceae on a long branch with uncertain position (Friedl, 1996;De Wever et al, 2009;Neustupa et al, 2011), while chloroplast multi-gene analyses placed Leptosira on a long branch, sister to the Chlorophyceae with moderate support (Turmel et al, 2009a;Turmel et al, 2009b;Zuccarello et al, 2009). Given the fact that Leptosira was the only trebouxiophycean representative outside the Chlorellales in these analyses, this relationship may be the result of systematic error in phylogenetic reconstruction (Turmel et al, 2009b).…”

“…All possible relationships have been hypothesized, depending on interpretation of ultrastructural characters, gene and taxon sampling, and phylogenetic methods used. Furthermore, the monophyly of the Trebouxiophyceae and Ulvophyceae has not been unequivocally demonstrated (Pröschold & Leliaert, 2007;Zuccarello et al, 2009). The unstable relationships exhibited among these three classes likely result from their antiquity and the short time span over which they diverged from one another (O'Kelly, 2007;Cocquyt et al, 2010b).…”

“…These datasets have mainly involved concatenated sequences of proteincoding genes that are shared among green algal chloroplast genomes. To date, 26 complete green algal plastid genomes have been sequenced and assembled (Wakasugi et al, 1997;Turmel et al, 1999b;Lemieux et al, 2000;Maul et al, 2002;Turmel et al, 2002b;Pombert et al, 2005;Turmel et al, 2005;Bélanger et al, 2006;de Cambiaire et al, 2006;Pombert et al, 2006;Turmel et al, 2006a;de Cambiaire et al, 2007;Lemieux et al, 2007;Robbens et al, 2007a;Brouard et al, 2008;Turmel et al, 2008;Turmel et al, 2009a;Turmel et al, 2009b;Zuccarello et al, 2009;Brouard et al, 2010;Brouard et al, 2011), in addition to more than 30 angiosperm plastid genomes (Soltis et al, 2009). Chloroplast genomes are particularly useful for phylogenetic reconstruction because of their relatively high and condensed gene content, in comparison to nuclear genomes.…”

New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data

“…The genus Leptosira, while mostly considered trebouxiophycean, has also been placed at the base of Chlorophyceae (Zuccarello et al, 2009;Turmel et al, 2009a,b). Contrary to these studies and consistent with recent publications on trebouxiophycean diversity (e.g., Neustupa et al, 2013a,b), our results place Leptosira with the majority of Trebouxiophyceae (Figures 2, 3).…”