CRYPTOMONAD NUCLEAR AND NUCLEOMORPH 18S RIBOSOMAL-RNA PHYLOGENY

Nuclear and nucleomorph 18S ribosomal RNA genes from six cryptomonads were amplified by the polymerase chain reaction and sequenced. Phyloge netic trees were constructed by distance, parsimony, and maximum likel ihood methods for all available cryptomonad nuclear and nucleomorph 18 S rRNA sequences. Nuclear and nucleomorph trees are largely congruent and dearly disprove the idea of polyphyletic origins for cryptomonad c hloroplasts. Both show the leucoplast-containing Chilomonas as the sis ter to all photosynthetic cryptomonads. Using 11 cryptomonad nucleomor ph sequences gives more convincing evidence than before that cryptomon ad nucleomorphs originated from a red alga and are not specifically re lated to Chlorarachnion nucleomorphs. Both trees show as a clade the g enera with nucleomorphs embedded in a chloroplast-envelope invaginatio n into the pyrenoid (Storeatula, Rhinomonas, Rhodomonas). This monophy ly 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 t he blue accessory pigment phycocyanin, form a clade, as do Guillardia and Cryptomonas Phi, both with the red pigment phycoerythrin. The nucl eomorph trees strongly show the blue Chroomonas/Komma dade as sister t o all red-pigmented genera, but nuclear sequences support this weakly, if at all, being sensitive to taxon sampling. Red and blue cryptomona ds probably diverged early by differential pigment loss. Nuclear seque nces provide no clear evidence for the nature of the host that engulfe d the ancestral symbiont. Our nuclear trees using an extensive selecti on of outgroups, and recent evidence from chloroplast DNA. are consist ent with but do not positively support the view that the closest relat ives of Cryptista (i.e. Cryptophyceae plus Goniomonadea) are the Chrom obiota (i.e. Haptophyta plus Heterokonta, the latter including heterok ont algae-phylum Ochrophyta), and that Cryptista and Chromobiota are a ppropriately classified as subkingdoms of the kingdom Chromista. Maxim um likelihood often groups Goniomonas with Chilomonas suggesting that Goniomonas may have lost both nucleomorph and plastid and that the cry ptist common ancestor was photosynthetic.