Cryptomonad nuclear and nucleomorph 18S rRNA phylogeny

Abstract

Nuclear and nucleomorph 18S ribosomal RNA genes from six cryptomonads were amplified by the polymerase chain reaction and sequenced. Phylogenetic trees were constructed by distance, parsimony, and maximum likelihood methods for all available cryptomonad nuclear and nucleomorph 18S rRNA sequences. Nuclear and nucleomorph trees are largely congruent and clearly disprove the idea of polyphyletic origins for cryptomonad chloroplasts. Both show the leucoplast-containing Chilomonas as the sister to all photosynthetic cryptomonads. Using 11 cryptomonad nucleomorph sequences gives more convincing evidence than before that cryptomonad nucleomorphs originated from a red alga and are not specifically related to Chloraraehnion nucleomorphs. Both trees show as a clade the genera with nucleomorphs embedded in a chloroplast-envelope invagination into the pyrenoid (Storeatula, Rhinomonas, Rhodomonas). This monophyly of embedded nucleomorphs supports the recent creation of the order Pyrenomonadales for such cryptomonads. Cryptomonads ancestrally having free nucleomorphs are much more diverse. Komma and Chroomonas, with the blue accessory pigment phycocyanin, form a clade, as do Guillardia and Cryptomonas ~, both with the red pigment phycoerythrin. The nucleomorph trees strongly show the blue Chroomonas/Komma clade as sister to all red-pigmented genera, but nuclear sequences support this weakly, if at all, being sensitive to taxon sampling. Red and blue cryptomonads probably diverged early by differential pigment loss. Nuclear sequences provide no clear evidence for the nature of the host that engulfed the ancestral symbiont. Our nuclear trees using an extensive selection of outgroups, and recent evidence from chloroplast DNA, are consistent with but do not positively support the view that the closest relatives of Cryptista (i.e. Cryptophyceae plus Goniomonadea) are the Chromobiota (i.e. Haptophyta plus Heterokonta, the latter including heterokont algae--phylum Ochrophyta), and that Cryptista and Chromobiota are appropriately classified as subkingdoms of the kingdom Chromista. Maximum likelihood often groups Goniomonas with Chilomonas, suggesting that Goniomonas may have lost both nucleomorph and plastid and that the cryptist common ancestor was photosynthetic.

Genetic diversity of goniomonads: an ancient divergence between marine and freshwater species

“…But whether Goniomonas is a sister to, or is nested within, the cryptophytes was less clear because some early trees showed it as a sister to Chilomonas paramecium Ehrenberg 1832 (Cavalier- Smith et al, 1996). Trees placing Goniomonas within cryptophytes were probably longbranch artifacts of the exceptionally long branch of G. truncata and of insufficient taxon sampling.…”

Nanoplankton protists from the western Mediterranean Sea. II. Cryptomonads (Cryptophyceae = Crptomonadea)

“…Subsequently, two attempts have been made to erect formal classification systems of the cryptomonads based on ultrastructural characters Lucas, 1993a, 1995;. More recently, molecular sequence data have been used to infer the phylogenetic relationships of the group and those within the group itself (McFadden et al, 1994;Cavalier-Smith et al, 1996;Marin et al, 1998;Hoef-Emden et al, 2002).…”

Fe-responsive accumulation of redox proteins ferredoxin and flavodoxin in a marine cryptomonad

“…One of the defining features of this group is a unique cellular compartment known as the nucleomorph, which appears to represent the vestigial nucleus of the original red algal symbiont (Douglas et al, 1991). Evidence derived from phylogenetic trees based on both cryptomonad nucleomorph and nuclear 18S rDNA support a monophyletic origin for this group (Cavalier-Smith et al, 1996;Deane et al, 2002).…”

“…Morphologically, their fine-structure is consistent with a secondary endosymbiotic origin (Gillott & Gibbs, 1980;Gibbs, 1981). Yet they are notable among chromophyte algae in that they retain a vestigial nucleus, the nucleomorph (Greenwood et al, 1977;Gillott & Gibbs, 1980;McFadden et al, 1997), that appears to be derived from an ancestral red algal endosymbiont (Douglas et al, 1991;Cavalier-Smith et al, 1996). As such, they have been the subject of extensive research into their evolutionary origins (Cavalier-Smith et al,1996;Deane et al, 2002).…”