The Exceptionally Large Chloroplast Genome of the Green Alga Floydiella terrestris Illuminates the Evolutionary History of the Chlorophyceae

Abstract

The Chlorophyceae, an advanced class of chlorophyte green algae, comprises five lineages that form two major clades (Chlamydomonadales + Sphaeropleales and Oedogoniales + Chaetopeltidales + Chaetophorales). The four complete chloroplast DNA (cpDNA) sequences currently available for chlorophyceans uncovered an extraordinarily fluid genome architecture as well as many structural features distinguishing this group from other green algae. We report here the 521,168-bp cpDNA sequence from a member of the Chaetopeltidales (Floydiella terrestris), the sole chlorophycean lineage not previously sampled for chloroplast genome analysis. This genome, which contains 97 conserved genes and 26 introns (19 group I and 7 group II introns), is the largest chloroplast genome ever sequenced. Intergenic regions account for 77.8% of the genome size and are populated by short repeats. Numerous genomic features are shared with the cpDNA of the chaetophoralean Stigeoclonium helveticum, notably the absence of a large inverted repeat and the presence of unique gene clusters and trans-spliced group II introns. Although only one of the Floydiella group I introns encodes a homing endonuclease gene, our finding of five free-standing reading frames having similarity with such genes suggests that chloroplast group I introns endowed with mobility were once more abundant in the Floydiella lineage. Parsimony analysis of structural genomic features and phylogenetic analysis of chloroplast sequence data unambiguously resolved the Oedogoniales as sister to the Chaetopeltidales and Chaetophorales. An evolutionary scenario of the molecular events that shaped the chloroplast genome in the Chlorophyceae is presented.

Phylogeny and Molecular Evolution of the Green Algae

“…But this is not a trend of the entire genus: the Nephroselmis olivacea ptDNA is 201 kb, a third of which represents noncoding nucleotides (Turmel et al, 1999b). The plastid genomes of the chlorophyceans Floydiella terrestris and Volvox carteri are ~525 kb and about 80% noncoding DNA (Brouard et al, 2010;Smith & Lee, 2010), making them almost 300 kb larger than any other available ptDNA sequence. Large plastid genomes are a common theme among chlorophycean algae: the sequenced ptDNAs from C. reinhardtii, Stigeoclonium helveticum, and Dunaliella salina are 204, 223, and 269 kb, respectively (Maul et al, 2002;Bélanger et al, 2006;Smith et al, 2010b), and gel electrophoresis results place the plastid genomes of both Chlamydomonas gelatinosa and Chlamydomonas moewusii at ~290 kb (Boudreau et al, 1994;Boudreau & Turmel, 1996).…”

“…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.…”

“…Phylogenetic analyses of nuclear rDNA data have suggested a sister relationship between the Chlamydomonadales and Sphaeropleales, with the Chaetophorales, Oedogoniales, and Chaetopeltidales forming early diverging clades with uncertain interrelationships (Booton et al, 1998a;Shoup & Lewis, 2003;Müller et al, 2004;Alberghina et al, 2006). Chloroplast multi-gene analyses identified two main lineages within the Chlorophyceae: a clade uniting the Chlamydomonadales and Sphaeropleales (CS clade), and a clade uniting the Oedogoniales, Chaetophorales, and Chaetopeltidales (OCC clade) Brouard et al, 2010). This dichotomy was independently supported by molecular signatures in chloroplast genes, such as presence of indels and transspliced introns.…”

“…Thus, it is significant that there are examples from each of the major green algal groups of species that have lost (or almost lost) their ptDNA inverted repeats. Examples include the charophyte green algae Staurastrum punctulatum and Zygnema circumcarinatum , the chlorophyceans F. terrestris and S. helveticum (Bélanger et al, 2006;Brouard et al, 2010), the prasinophytes P. provasolii and Monomastix (Turmel et al, 2009a), the ulvophyte B. hypnoides (Lü et al, 2011), and the trebouxiophytes L. terrestris and Helicosporidium sp. (de Koning & Keeling, 2006;de Cambiaire et al, 2007).…”

The Plastid Genome of Polytoma uvella Is the Largest Known among Colorless Algae and Plants and Reflects Contrasting Evolutionary Paths to Nonphotosynthetic Lifestyles

“…The P. uvella ptDNA has an overall noncoding content of 73%, which is on par with other bloated plastid genomes, including those of the green algae V. carteri and Floydiella terrestris (Brouard et al, 2010), two of the largest ptDNAs on record, but is in stark contrast to the compact ptDNAs typical of most colorless algae (Table I). At approximately 5% noncoding, the plastid genomes of Helicosporidium sp.…”