A eukaryotic genome of 660 kb: electrophoretic karyotype of nucleomorph and cell nucleus of the cryptomonad alga,<i>Pyrenomonas salina</i>

Eschbach, Stefan; Hofmann, Chr; Maier, Uwe‐G.; Sitte, Peter; Hansmann, Paul

doi:10.1093/nar/19.8.1779

Cited by 73 publications

(31 citation statements)

References 23 publications

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“…We have therefore sequenced both the nuclear and the nucleomorph 18S rRNA genes of six diverse cryptomonads in order to see whether or not the trees derived from the two separate genomes are congruent. Together with previous data from five other cryptomonads (Douglas et al, 1991;Eschbach et al, 1991a;Maier el al., 1991;Cavalier-Smith et al, 1994) this enables us to clarify several important aspects of cryptomonad phylogeny. We particularly wished to examine two key questions.…”

Section: Introductionsupporting

confidence: 77%

Cryptomonad nuclear and nucleomorph 18S rRNA phylogeny

Cavalier‐Smith

Couch

Thorsteinsen

et al. 1996

European Journal of Phycology

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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.

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Section: Introductionsupporting

confidence: 77%

Cryptomonad nuclear and nucleomorph 18S rRNA phylogeny

Cavalier‐Smith

Couch

Thorsteinsen

et al. 1996

European Journal of Phycology

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“…2 (CCMP 242)] were cultured as described (15), and total DNA was isolated as described (19). Nuclei were isolated as described (12). Universal cytoplasmic-type srRNA gene primers (5'-TACCTGGTGGATCCT-GCCAG-3' and 5'-TGATCCTTCTGCAGGTTCACCTAC-3') were used to amplify srRNA genes by PCR (10).…”

Section: Methodsmentioning

confidence: 99%

“…Flagellate cells of Chlorarachnion sp. 1 were embedded in plugs of low-gellingtemperature agarose at 1.4 x 108 cells per ml and then digested as described (12). Chromosomal DNAs were electrophoresed in 1% agarose (SeaKem LE, FMC) in a CHEF DRII apparatus (Bio-Rad) at 170 V with a 20-sec pulse for 30 h. DNA was transferred to ZetaProbe nylon membrane (Bio-Rad) as recommended by the manufacturer.…”

Section: Methodsmentioning

confidence: 99%

Evidence that an amoeba acquired a chloroplast by retaining part of an engulfed eukaryotic alga.

McFadden

Gilson

Hofmann

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

142

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“…Far and away the most extreme examples of eukaryotic genome reduction are the ''nucleomorph'' genomes of cryptophytes and chlorarachniophytes. Nucleomorphs are the relic nuclei of algal endosymbionts that became permanent inhabitants of nonphotosynthetic eukaryotic host cells (3)(4)(5). Through the combined effects of genome compaction and intracellular gene transfer, the nucleomorph genomes of cryptophytes and chlorarachniophytes have shrunk to a fraction of the size of the algal nuclear genomes from which they are derived and, thus, represent a fascinating system for studying the process of genome evolution.…”

mentioning

confidence: 99%

“…Preliminary karyotype diversity studies have revealed considerable size variation, with estimated nucleomorph genome sizes ranging from Ϸ450 to 845 kbp in cryptophytes and Ϸ330-610 kbp in chlorarachniophytes (4,(10)(11)(12)(13)(14). The presence of three chromosomes is thus far a universal feature of nucleomorph genomes (3,12,14), as is the existence of subtelomeric rDNA repeats.…”

mentioning

confidence: 99%

Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function

Lane

Heuvel

Kozera³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

137

167

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Nucleomorphs are the remnant nuclei of algal endosymbionts that took up residence inside a nonphotosynthetic eukaryotic host. The nucleomorphs of cryptophytes and chlorarachniophytes are derived from red and green algal endosymbionts, respectively, and represent a stunning example of convergent evolution: their genomes have independently been reduced and compacted to <1 megabase pairs (Mbp) in size (the smallest nuclear genomes known) and to a similar three-chromosome architecture. The molecular processes underlying genome reduction and compaction in eukaryotes are largely unknown, as is the impact of reduction/ compaction on protein structure and function. Here, we present the complete 0.572-Mbp nucleomorph genome of the cryptophyte Hemiselmis andersenii and show that it is completely devoid of spliceosomal introns and genes for splicing RNAs-a case of complete intron loss in a nuclear genome. Comparison of H. andersenii proteins to those encoded in the slightly smaller (0.551-Mbp) nucleomorph genome of another cryptophyte, Guillardia theta, and to their homologs in the unicellular red alga Cyanidioschyzon merolae reveal that (i) cryptophyte nucleomorph genomes encode proteins that are significantly smaller than those in their free-living algal ancestors, and (ii) the smaller, more compact G. theta nucleomorph genome encodes significantly smaller proteins than that of H. andersenii. These results indicate that genome compaction can eliminate both coding and noncoding DNA and, consequently, drive the evolution of protein structure and function. Nucleomorph proteins have the potential to reveal the minimal functional units required for basic eukaryotic cellular processes.endosymbiosis ͉ genome evolution ͉ genome reduction

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A eukaryotic genome of 660 kb: electrophoretic karyotype of nucleomorph and cell nucleus of the cryptomonad alga,Pyrenomonas salina

Cited by 73 publications

References 23 publications

Cryptomonad nuclear and nucleomorph 18S rRNA phylogeny

Cryptomonad nuclear and nucleomorph 18S rRNA phylogeny

Evidence that an amoeba acquired a chloroplast by retaining part of an engulfed eukaryotic alga.

Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function

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