Vol 451 | 21 February 2008 | doi:10.1038/nature06635
ARTICLES
A photosynthetic alveolate closely related
to apicomplexan parasites
Robert B. Moore1,2*, Miroslav Obornı́k3*, Jan Janouškovec3, Tomáš Chrudimský3, Marie Vancová3, David H. Green4,
Simon W. Wright5, Noel W. Davies6, Christopher J. S. Bolch7, Kirsten Heimann8, Jan Šlapeta9,
Ove Hoegh-Guldberg10, John M. Logsdon Jr2 & Dee A. Carter1
Many parasitic Apicomplexa, such as Plasmodium falciparum, contain an unpigmented chloroplast remnant termed the
apicoplast, which is a target for malaria treatment. However, no close relative of apicomplexans with a functional
photosynthetic plastid has yet been described. Here we describe a newly cultured organism that has ultrastructural features
typical for alveolates, is phylogenetically related to apicomplexans, and contains a photosynthetic plastid. The plastid is
surrounded by four membranes, is pigmented by chlorophyll a, and uses the codon UGA to encode tryptophan in the psbA
gene. This genetic feature has been found only in coccidian apicoplasts and various mitochondria. The UGA-Trp codon and
phylogenies of plastid and nuclear ribosomal RNA genes indicate that the organism is the closest known photosynthetic
relative to apicomplexan parasites and that its plastid shares an origin with the apicoplasts. The discovery of this organism
provides a powerful model with which to study the evolution of parasitism in Apicomplexa.
Alveolata Cavalier-Smith, 1991 (emended by ref. 1)
Chromerida phyl. nov.
Chromera velia gen. et sp. nov.
Etymology. Chromera (feminine), derived from the English words
chromophore and meront, because in pure culture the pigmented
plastid was inherited through cell division; velia (feminine), a modern Italian proper name, meaning veiled or concealed (Supplementary Information).
Holotype/hapantotype. Z.6967 (Australian Museum, Sydney), preserved culture embedded in PolyBed 812 (electron micrographs
shown in Fig. 1a, b) and separately in absolute ethanol. The culture
is NQAIF136 (North Queensland Algal Culture and Identification
Facility, James Cook University, Townsville, Australia). The clonal
culture consists of dividing immotile organisms. Culture submission
date, 25 February 2004; culture isolation date, 13 December 2001;
isolator, R.B.M.
Locality. Scleractinian coral Plesiastrea versipora (type host;
Lamarck, 1816) (Metazoa: Cnidaria: Faviidae) obtained from
Sydney Harbour, New South Wales, Australia (latitude 33u 509
38.7699 S; longitude 151u 169 4499 E) at ,3-m depth. Collection date,
7 December 2001. Collectors: T. Starke-Peterkovic and L. Edwards.
Referred material. Additional cultures are CCAP 1602/1 (Culture
Collection of Algae and Protozoa, Scottish Association of Marine
Science, UK) and CCMP2878 (Provasoli-Guillard Center for
Culture of Marine Phytoplankton, Maine, USA).
Diagnosis. Unicellular (Fig. 1a). The immotile life stage reproduces
by binary division (Fig. 1b), but is not restricted to binary division.
The immotile life stage is spherical to sub-spherical, 5–7 mm in diameter in the G1 phase of the cell cycle. Cell diameter is up to 9.5 mm in
other cell cycle phases. A golden-brown, cone-shaped plastid is present. Immediately after completion of binary division, nascent cells
contain a single plastid only. Thylakoid lamellae are in stacks of three
or more (Fig. 1c). The plastid is bounded by four membranes (Fig. 1d)
and contains chlorophyll a, but no other chlorophylls. A micropore
is present (Fig. 1c). Internal cilium/cilia are present and anchored
at the cell periphery, extending to the periplastidal compartment
(Fig. 1a, f, g). Cortical alveoli are flattened, with underlying microtubules (Fig. 1e). The position of attachment of internal cilium
to the cell periphery is defined as the apex of the immotile cell.
There is a single, large mitochondrion ,1 mm in diameter (Fig. 1a).
Mitochondrial cristae are lamellar, ampulliform and tubular in
structure. Vesicles of diameter ,1 mm attach to and surround the
large mitochondrion. The cell wall surface is smooth, with a raised
ridge ,85 nm wide, extending around an incomplete circle and
forking periodically (Supplementary Information). Chromera velia
is free-living or associated with stony corals; it is the type species
of the phylum Chromerida. Chromerida differ from all known
alveolates1 (Supplementary Information) in having a photosynthetic
secondary plastid bearing chlorophyll a, but no chlorophyll c2.
Plastids of alveolates and their medical significance
The alveolates are a major lineage of protists that are defined by the
possession of subsurface alveoli (flattened membrane-bound vesicles) supported by microtubules, as well as the presence of micropores and mitochondria with ampulliform or tubular cristae1,3.
Alveolates are divided into three main phyla: the ciliates, apicomplexans and dinoflagellates. The group Apicomplexa1 (Levine, 1970;
emended by Adl et al. 2005 (ref. 1)) is composed mostly of parasites
that are united by the possession of a set of secretory organelles
1
School of Molecular and Microbial Biosciences, University of Sydney, Darlington, New South Wales 2006, Australia. 2Roy J. Carver Center for Comparative Genomics, Department of
Biological Sciences, University of Iowa, Iowa City, Iowa 52242-1324, USA. 3Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Parasitology, and University of
South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic. 4Scottish Association for Marine Science, Dunstaffnage Marine Laboratory Oban, Argyll
PA37 1QA, UK. 5Australian Antarctic Division, Kingston, Tasmania 7050, Australia. 6Central Science Laboratory, University of Tasmania, Hobart, Tasmania 7001, Australia. 7School of
Aquaculture, University of Tasmania, Launceston, Tasmania 7250, Australia. 8School of Marine and Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia.
9
Faculty of Veterinary Science, University of Sydney, Camperdown, New South Wales 2006, Australia. 10Centre for Marine Studies, University of Queensland, St Lucia, Queensland
4072, Australia.
*These authors contributed equally to this work.
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ARTICLES
NATURE | Vol 451 | 21 February 2008
b
a
*
n1
pl1
n
pl1
pl1
iinv
cf
cf
cf
pl
m
m
pl
pl2
pl2
pl2
n2
ic
ic
*
c
mi
pl
cw
mv
d
pl
pc
e
cw
f
ic
g
pl
pl
g
ic1
ic2
bb1
Figure 1 | Ultrastructure of new alveolate Chromera velia. a, Interphase (scale
bar, 2 mm). iinv, interphase invagination (black arrow); m, mitochondrion; n,
nucleus; pl, plastid. b, Binary division. The apex of each daughter cell is marked
by an asterisk. The mitochondrion of the mother cell is centrally positioned at
the terminator of the cleavage furrow, between the nuclei of daughter cells 1
and 2 (scale bar, 2 mm). cf, cleavage furrow. c, Micropore (mi) and thylakoid
lamellae. The micropore is an invagination of the plasma membrane. An
associated vesicle in the cytoplasm is indicated (mv, micropore-associated
vesicle). Thylakoid lamellae in the plastid are in sets of three (white arrows) or
more (scale bar, 200 nm). cw, cell wall. d, The two pairs of plastid membranes
separate at the periplastidal compartment (white triangles). The outer pair
forms the periplastidal compartment (scale bar, 200 nm). pc, periplastidal
compartment. e, Alveoli and supporting microtubules. Alveoli lying beneath
the plasma membrane abut each other closely (at black arrows) and are
underlain by microtubules (white arrow) (scale bar, 500 nm). f, Maintenance
of the plastid (pl) in a cone shape is aided by one or more internal cilia (ic, white
triangle) anchored at the apex of the cell (scale bar, 2 mm). g, Magnification of
boxed area in f. Internal cilium ic1 extends inward from basal body bb1 (white
triangle), which is attached to the cell periphery. ic1 and bb1 join at a terminal
plate (black arrow). ic2 (white arrow) emerges perpendicular to ic1 (scale bar,
500 nm). a, b, Hapantotype Z.6967 (Australian Museum, Sydney).
underlying an oral structure at the anterior apex of the cell4 (the
‘apical complex’), and other characters. Within the phylum is a
monophyletic subgroup of obligate parasites that comprises some
6,000 taxa5. These present a major burden to livestock and human
health. Many contain a relic plastid termed the apicoplast6. Among
the apicomplexans, it is specifically hemosporidians, piroplasms
(both groups are blood parasites, including Plasmodium, that cause
malaria) and coccidians (for example, Toxoplasma gondii7 and the
veterinary pathogen Eimeria) that possess an apicoplast. Because
animals do not possess plastids, the apicoplast represents an opportunity to target these parasites with treatments that are relatively
harmless to mammalian hosts8.
The reduced 35-kilobase genome and imported proteome of the
Plasmodium apicoplast have been exhaustively studied. Several
critical pathways are localized in the apicoplast, including fatty acid
and isoprenoid biosynthesis6. However, not all apicomplexans
possess this organelle. No evidence of a plastid has been found in
Gregarina, the only gregarine examined so far9. Similarly, the waterborne parasite Cryptosporidium lacks an apicoplast10,11. Finally, there
is no published evidence for apicoplasts in colpodellids, a group of
non-parasitic apicomplexans that possess an apical complex of
organelles used for predation on algal and protist prey4,12.
In the absence of an extant alga that represents the ancestral photosynthetic state of these diverse apicomplexans, the evolutionary
descent of the apicoplast has instead been indicated by taxonomic
and phylogenetic affiliation of apicomplexans to particular algae.
Gene phylogenies relate the apicoplasts to the chloroplasts of a subset
of dinoflagellate algae—those that are pigmented by the chromophore peridinin13,14. It is thought that the common ancestor of peridinin dinoflagellates and apicomplexans possessed a chromalveolate
plastid containing the specific combination of chlorophyll a and
chlorophyll c13,15. Whereas peridinin dinoflagellates retained the
plastid, degeneration of the photosynthetic chromalveolate plastid
occurred independently in many other dinoflagellates and also
occurred independently in apicomplexans16. In a range of dinoflagellates, photosynthetic plastids were ingested and replaced the chromalveolate plastid16. In other dinoflagellates, the chromalveolate plastid
was lost and not replaced, resulting in heterotrophy4,15,17. In parasitic
apicomplexans the plastid remains, but in a non-photosynthetic form.
Here we show that C. velia is a relative of parasitic apicomplexans and
colpodellids, and bears a photosynthetic plastid that is related most
closely to apicoplasts but also to peridinin dinoflagellate plastids,
affirming a common ancestry. Chromera velia can live independently
of its host and is easily maintained in culture. As well as providing a
model to study apicomplexan evolution, we predict that C. velia will
be of practical use in high-throughput screening of prospective antiapicoplast drugs.
Evolutionary position of Chromera velia
The three ultrastructural features diagnostic of alveolates1,3 are all
present in C. velia: first, a micropore occurs in the cell periphery
(Fig. 1c); second, subsurface alveoli are present and supported by
microtubules (Fig. 1e); and third, the mitochondrion (Fig. 1a) contains ampulliform and tubular cristae (Supplementary Information).
Molecular phylogenetic analyses of nuclear genes showed that
C. velia is more closely related to apicomplexan parasites than to
photosynthetic dinoflagellates. In bayesian and maximum likelihood
analyses of nuclear large subunit (LSU) rDNA sequences, C. velia
branched at the root of the Apicomplexa (Fig. 2a), with this position
corroborated by a topology test (Fig. 2b) and by slow–fast analysis
(Supplementary Information). Phylogeny of nuclear small subunit
(SSU) rDNA sequences also supported a close relationship between
C. velia and apicomplexans, with the new taxon branching at the root
of colpodellids (Fig. 2c). Although the position of Chromera on this
tree had relatively low bootstrap and posterior probability support
(maximum likelihood bootstrap 68, posterior probability 0.90),
960
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ARTICLES
NATURE | Vol 451 | 21 February 2008
Alexandrium catenella
Alexandrium tamarense
Alexandrium affine
Alexandrium minutum
0.71/Lingulodinium polyedrum
Dinoa
1.00/53 Prorocentrum donghaiense
flagellates
Prorocentrum micans
Pfiesteria piscicida
1.00/99
Akashiwo sanguinea
1.00/95
Prorocentrum micans
2
Perkinsus chesapeaki
Perkinsus andrewsi
Perkinsids
Perkinsus atlanticus
Hammondia hammondi
Toxoplasma gondii
Coccidia
Neospora caninum
Besnoitia besnoiti
(Apicomplexans)
Isospora felis
Frenkelia microti
Sarcocystis neurona
Sarcocystis muris
1
Eimeria tenella
0.99/84
Chromera velia
Tetrahymena thermophila
Tetrahymena pyriformis
Ciliates
Paramecium tetraurelia
Nannochloropsis salina
Dictyocha speculum
Stramenopiles
Hyphochytrium catenoides
Phytophthora megasperma
0.65/Guillardia theta
Cryptophyte
0.1
b
bp
pp
kh
sh
wkh
wsh
Topology 1
0.989 0.991
0.990
1.00
0.988
0.988
0.988
0.988
Topology 2
0.011 0.009
0.010 9x10
0.012
0.012 0.012
0.012
Nuclear LSU rDNA
au
np
−13
0.87/91 Heterocapsa rotundata
Heterocapsa pygmaea
Scrippsiella trochoidea
Alexandrium pseudogonyaulax
1.00/79
Gyrodinium dorsum
Prorocentrum
emarginatum
0.92/Peridinium balticum
0.95/Kryptoperidinium foliaceum
Dinoflagellates
Dinophysis norvegica
Prorocentrum minimum
Cryptoperidiniopsis brodyi
0.90/53
Gyrodinium impudicum
Amphidinium semilunatum
Amoebophrya sp.
Eukaryotic clone OLI11005
0.99/75
Hematodinium sp.
3
Noctiluca scintillans
0.64/98 Perkinsus atlanticus
Perkinsus atlanticus
Perkinsids
Perkinsus sp.
Perkinsus marinus
Caryospora bigenetica
Apicomplexans
Eimeria alabamensis
1.00/100
Toxoplasma gondii
Theileria buffeli
1.00/Babesia gibsoni
Monocystis agilis
0.99/54
Ophriocystis elektroscirrha
0.98/Selenidium terebellae
Cryptosporidium serpentis
0.93/54
Marine parasite from Tridacna crocea
Marine clone from Ammonia beccarii
Environmental
sequence AF372772
2
Colpodella
edax
1.00/100
Environmental sequence AF372785
Colpodellids
0.99/64
Environmental sequence AF372786
0.89/56
Colpodella sp. ATCC 50594
1
Voromonas pontica
0.90/68
0.99/58
Chromera velia
1.00/100
1.00/80
Urocentrum turbo
Furgasonia blochmanni
Oxytricha
nova
0.99/83
Ciliates
Didinium nasutum
Protocruzia sp.
1.00/99
Blepharisma americanum
Thraustochytrium multirudimentale
Mallomonas striata
Stramenopiles
Costaria costata
0.1
c
d
bp
pp
sh
wkh
wsh
0.631
0.709 0.743
0.856
0.743
0.901
0.150 0.351
0.358
0.291
0.257
0.610
0.257
0.491
0.006 0.011
0.011 2x10−6
0.039
0.044
0.039
0.046
au
np
Nuclear SSU rDNA
Topology 1
0.955 0.634
Topology 2
Topology 3
kh
Neospora caninum
Apicoplasts
Toxoplasma gondii
Hyaloklossia lieberkuehni
Coccidians
Sarcocystis muris
e
Eimeria tenella
Eimeria sp.
Haemosporidians
Eimeria meleagrimitis
Plasmodium falciparum
Plasmodium vivax
0.99/54
1.00/99
Babesia bovis
Piroplasmids
Babesia bigemina
0.90/52
Hepatozoon catesbianae
Chromera velia
Coccidian
Euglena gracilis
Euglenozoans
Astasia longa
Dinoflagellates
Karlodinium veneficum
0.58/77
Karlodinium veneficum
with haptophyteIsochrysis sp.
0.92/derived plastid
Ochrosphaera
sp.
Haptophytes
0.68/82
Chrysochromulina sp.
0.98/Karenia sp.
Dinoflagellates
Karenia mikimotoi
0.71/with haptophyteKarenia mikimotoi
Karenia brevis
derived plastid
Pavlova gyrans
Haptophyte
Odontella sinensis
Bacillariophyte (diatom)
Dinophysis acuminata
Dinoflagellates with
1.00/71 Dinophysis norvegica
cryptophyte-derived plastid
Dinophysis tripos
Guillardia theta
Cryptophyte
Porphyra purpurea
Red alga
Epifagus virginiana
Nicotiana tabacum
Plants and green algae
Chlorella ellipsoidea
0.97/64
Chlorella vulgaris
Cyanothece
sp.
0.91/79
Gloeocapsa sp.
Cyanobacteria
Rhopalodia gibba
Synechocystis sp.
0.1
0.56/65
Figure 2 | Nuclear and plastid phylogenies of Chromera velia. a, Bayesian
phylogenetic tree of nuclear LSU rDNA inferred from 2,740 characters
(GenBank accession EU106870). b, Topology tests of the placement of the C.
velia branch with respect to branches of the nuclear LSU rDNA tree.
Numbered branches are indicated in a. Topology test results are: the P-value
for the approximately unbiased test (au) calculated from the multiscale
bootstrap; the non-parametric bootstrap probability calculated from the
multiscale bootstrap (np); the bootstrap probability calculated in the nonmultiscale manner (bp); the bayesian posterior probability calculated by the
bayesian-information-criterion approximation (pp); and the P-values of the
Kishino–Hasegawa test (kh), the Shimodaira–Hasegawa test (sh), the
weighted Kishino–Hasegawa test (skh) and the weighted
Heterocapsa triquetra
Heterocapsa pygmaea
Alexandrium tamarense
Lingulodinium polyedrum
Scrippsiella trochoidea
f
Symbiodinium from Tridacna
Thoracosphaera heimii
0.96/50
Amphidinium carterae
1
Prorocentrum micans
0.60/Chromera velia
Pylaiella littoralis
0.87/62
Ectocarpus siliculosus
Peridinin
0.61/- 2
Padina crassa
dinoflagellates
Dictyota pardalis
Heterosigma akashiwo
Stramenopiles
0.97/65
Heterosigma carterae
3
Bumilleriopsis filiformis
0.93/56
Vaucheria litorea
Odontella sinensis
0.89/97
0.98/62 Isochrysis sp.
0.57/53 Emiliania huxleyi
0.83/- Pleurochrysis carterae
Phaeocystis antarctica
Haptophytes
Prymnesium parvum
0.69/Pavlova lutheri
Pavlova gyrans
0.90/Karenia brevis
Dinoflagellates with haptophyteKarenia mikimotoi
derived plastid
0.72/Palmaria palmata
0.61/1.00/- 0.69/- Stylonema alsidii
Rhodosorus marinus
Rhodophytes (red algae)
0.84/Compsopogon caeruleus
0.91/60
Porphyridium aerugineum
Bangia fuscopurpurea
0.77 Rhodomonas abbreviata
Cryptophytes
0.97 Pyrenomonas helgolandii
Dinoflagellates with
Dinophysis norvegica
cryptophyte-derived
Chroomonas
plastid
Cryptophytes
Chilomonas paramecium
Dixoniella grisea
Rhodophytes
Rhodella violacea
0.1
0.99/84
0.80/56
g
bp
pp
kh
sh
wkh
wsh
0.698 0.972
0.705
0.843
0.705
0.808
0.285 0.289 0.027
Topology 3 0.041 0.016 0.013 0.001
0.295
0.368
0.295
0.416
0.074
0.144 0.074
0.144
au
PsbA
Topology 1 0.736
Topology 2 0.334
np
0.699
Shimodaira–Hasegawa test (wsh). c, Bayesian phylogenetic tree of nuclear
SSU rDNA inferred from 1,285 characters (GenBank accession DQ174732).
d, Topology tests of the placement of the C. velia branch with respect to
branches of the nuclear SSU rDNA tree. Numbered branches are indicated in
c. e, Bayesian phylogenetic tree of plastid SSU rDNA gene sequences inferred
from 811 characters (GenBank accession EU106871). f, Bayesian
phylogenetic tree of the PsbA photosynthesis protein inferred from 319
characters (GenBank accession EU106869). g, Topology tests of the
placement of the C. velia branch with respect to branches of the PsbA tree.
Numbered branches are indicated in f. On all trees, black stars indicate
branches with bayesian posterior probabilities higher than 0.99 and
maximum likelihood bootstrap support higher than 90%.
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topology tests rejected alternative placement of Chromera at the
root of dinozoans (Fig. 2d).
The lineage of the C. velia plastid was analysed using plastid rDNA
and PsbA, a plastid protein that is part of photosystem II. In the
phylogenetic analysis of plastid SSU rDNA, the C. velia chloroplast
branched at the root of the apicoplasts with good support (Fig. 2e). It
was not possible to include sequences from the peridinin-pigmented
plastids of dinoflagellates in the plastid SSU rDNA analyses because
their high divergence caused their position in trees to be unstable.
The PsbA sequence of C. velia was found to be conserved when
compared with that of other photosynthetic eukaryotes (Supplementary Information), and phylogenetic analysis of PsbA was therefore
restricted to relevant taxa to avoid the effects of homoplasy across
unrelated lineages. Taxa were selected based on the strong relationships shown between C. velia, dinoflagellates and stramenopiles on
the nuclear rDNA trees. The selected set included dinoflagellates,
other chromalveolates and rhodophytes (Fig. 2f). Apicoplasts could
not be included as they do not possess the psbA gene. Although
maximum likelihood support across the PsbA protein tree was limited, there was significant bayesian support for known relationships,
such as a grouping of stramenopile and dinoflagellate secondary
plastids (posterior probability 0.97, maximum likelihood 65), and
a grouping of haptophyte secondary plastids as neighbour to these
two (posterior probability 0.99, maximum likelihood 90). The analysis supported C. velia as a relative of peridinin dinoflagellate plastids (posterior probability 0.96, maximum likelihood 50). Topology
testing (Fig. 2g) corroborated the most likely placement of the C. velia
plastid as closest sister group to the plastids of peridinin dinoflagellates, as was expected given that apicomplexans were not included in
the analysis.
Unique features of the Chromera velia plastid
The psbA gene of C. velia contains an unusual codon that links the
plastid to the apicoplast lineage. All other eukaryotic algae use UGG
codons to encode tryptophan at seven conserved positions in the
gene. The C. velia gene instead uses UGA codons at these positions
(Supplementary Information). The UGA-Trp codon is unprecedented in any photosynthetic plastid and has only been found in the
apicoplasts of coccidians and in various mitochondria6,18.
The C. velia plastid contains thylakoid lamellae in stacks of three
or more (Fig. 1c), resembling the arrangement in the plastids of
peridinin-pigmented dinoflagellates19. It displays novel pigmentation, with chlorophyll a, violaxanthin and a novel carotenoid as
the major components, and b,b-carotene as a minor component
(Supplementary Information). No other chlorophylls are present.
Mass spectrometry analysis indicated that the novel carotenoid is
an isomer of isofucoxanthin (Supplementary Information). This
finding is consistent with the Chromera plastid being red-derived,
as isomers of isofucoxanthin are absent from plastids of the green
lineage2. Pulse amplitude modulation fluorescence analysis confirmed that photosynthesis occurs in Chromera (Supplementary
Information). Assuming that the apicomplexan–dinoflagellate group
was ancestrally photosynthetic, the absence of chlorophyll c in C.
velia was unexpected, as peridinin dinoflagellates normally possess
this pigment. We propose that secondary loss of chlorophyll c could
have occurred in early apicomplexans.
An ultrastructural feature in common between the C. velia plastid
and apicoplasts is the number of surrounding membranes. It is
generally presumed that the number of membranes surrounding a
stable plastid can decrease but not increase during its evolutionary
specialization20. The C. velia plastid is surrounded by four membranes (Fig. 1d). Reports vary in their estimates of the number of
membranes surrounding apicomplexan plastids. Three-dimensional
reconstruction of the P. falciparum apicoplast indicated three membranes21, supplemented with additional inner and outer membrane
complexes. A similar reconstruction of the apicoplast of the coccidian T. gondii found spatial alternation of two and four membranes22.
By comparison, the plastids of peridinin dinoflagellates are surrounded by three membranes19,20. We suggest that the four membranes bounding the C. velia plastid may represent the number
surrounding the ancestor of apicoplasts and peridinin dinoflagellate
plastids.
Hemosporidians and piroplasms
Chromera velia
Colpodellids
Coccidians
Cryptosporidium
Gregarina
Plastid
X
No evidence
for a plastid
X
R
Loss of
photosynthesis
Replacement
of plastid
X
Other
dinozoans
Origination
of UGA-Trp UGG
UGA
readthrough
Chlorophyll types
a, a + c in photosynthesis
X
Loss of
chl. c
Peridinin
dinoflagellates
R
METHODS SUMMARY
X
a
UGG
UGG
UGG-Trp plastid
UGG
UGA
UGG+UGA-Trp plastid
a+c
Concluding remarks
Phylogenetic analyses support the description of Chromera velia as an
alveolate, possessing a photosynthetic plastid that lies in the same
secondary endosymbiotic lineage as apicoplasts. The ultrastructure
and photosynthetic pigment profile of C. velia are consistent with a
chromalveolate-affiliated ancestry. Figure 3 presents a model of the
evolutionary history of C. velia, apicomplexans and dinoflagellates
based on the phylogeny of the nuclear and plastid lineages and the
retention or loss of plastid characteristics. Chromera velia represents
the closest known photosynthetic relative of apicomplexan parasites.
Ancestor of apicomplexans
and dinozoans
Figure 3 | Evolution of Chromera velia, apicomplexans and dinoflagellates.
The path in green traces the maintenance of photosynthesis. Characteristics
of the terminal nodes of coccidia, hemosporidians and piroplasms are
generalized. The gregarine shown is Gregarina niphandroides9. The
Cryptosporidium species represented is C. parvum11,25. ‘Other dinozoans’
includes non-photosynthetic species: Perkinsus atlanticus (filled black circle,
plastid present26) and Oxyrrhis marina (open circle, no plastid evident27).
The dinozoan branch bearing ‘replaced plastids’ is a symbolic branch
representing many such branches that obtained tertiary plastids
independently. Heterotrophic dinoflagellates have characters as for Oxyrrhis
marina. The tree is a consensus of data presented in this paper and other
published relationships10,12,13,28–30.
Chromera velia was isolated from the stony coral Plesiastrea versipora (Faviidae)
from Sydney Harbour (Australia) by a variation of a procedure23 normally used
to isolate intracellular symbionts of the genus Symbiodinium (Supplementary
Information). Unicellular lines were generated by streaking raw colonies onto an
agar-gelled minimal growth medium, picking single colonies and regrowing in
liquid medium (Supplementary Information). Genomic DNA was extracted and
genes (nuclear SSU and LSU rDNA, and plastid SSU rDNA and psbA) were
amplified and sequenced. Purity of cultures was checked by sequencing multiple
nuclear SSU rDNA clones from each unialgal line (Supplementary Information).
Sequences were aligned, and phylogenetic analyses were performed using maximum likelihood and bayesian inference. Selected data sets were analysed using a
slow–fast method. Specimens for transmission electron microscopy (TEM) were
prepared using a freeze-substitution method24 and examined by TEM. Scanning
electron microscopy (SEM) specimens were prepared using standard methods
(Supplementary Information). Pigments were extracted and analysed by a combination of high-performance liquid chromatography (HPLC), ultraviolet and
visible (UV/Vis ) spectra analysis and mass spectrometry (MS), and were identified by comparison of their retention times and spectra to those of mixed
standards obtained from known cultures (Supplementary Information).
962
©2008 Nature Publishing Group
ARTICLES
NATURE | Vol 451 | 21 February 2008
Received 15 September 2007; accepted 9 January 2008.
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Supplementary Information is linked to the online version of the paper at
www.nature.com/nature.
Acknowledgements This work was supported by an ARC grant to D.A.C. and
O.H.-G.; an ABRS grant to D.A.C.; grants from the Czech Science Foundation,
Academy of Sciences of the Czech Republic and Czech Ministry of Education to
M.O.; University of Iowa start-up funds and an NSF grant to J.M.L.; and a University
of Tasmania Institutional Research grant to C.J.S.B. We thank A. McMinn for pulse
amplitude modulation data, A. Simpson for analytical suggestions, R. Andersen for
culture backup, and A. Polaszek and M. Garland for taxonomic opinions.
Author Contributions R.B.M. isolated the strain while in the D.A.C. laboratory, then
while in the J.M.L. laboratory designed the AToL SSU primers and the psbA primers,
cloned and sequenced multiple copies of the SSU rRNA gene, a copy of the plastid
SSU rRNA gene and initial sections of the psbA and LSU rRNA genes, then assigned
precedented methods for culture fixation, and wrote and finalized the draft of the
paper; M.O. led and performed phylogenetic analyses of the sequence data, cloned
and sequenced a copy of the plastid SSU rDNA gene using different primers than
R.B.M., and co-wrote the draft of the paper; M.O. and M.V. performed the TEM and
SEM data collection; J.J. and T.C. cloned and sequenced near full-length LSU rDNA
and psbA genes and undertook extensive phylogenetic analysis; T.C. performed
mito-red staining; S.W.W. and N.W.D. performed pigment analysis and interpreted
pigment data; R.B.M., K.H., C.J.S.B. and J.S. interpreted TEM data and assigned
taxonomy; K.H. and R.B.M. performed light microscopy; R.B.M., M.O., T.C., K.H.,
D.H.G. and C.J.S.B. maintained cultures. D.H.G. cloned and sequenced the LSU
rRNA gene, using different PCR primers than T.C. and J.J.; R.B.M., M.O., D.H.G.,
K.H., J.S., O.H.-G., J.M.L., C.J.S.B. and D.A.C. designed research, interpreted
evolutionary, ecological and microbiological data, and performed extensive editing
and revision.
Author Information Reprints and permissions information is available at
www.nature.com/reprints. Correspondence and requests for materials should be
addressed to D.A.C. ([email protected]).
963
©2008 Nature Publishing Group
CORRECTIONS & AMENDMENTS
NATUREjVol 452j17 April 2008
CORRIGENDUM
ERRATUM
doi:10.1038/nature06871
doi:10.1038/nature06898
A photosynthetic alveolate closely related to Strong dispersive coupling of a high-finesse
cavity to a micromechanical membrane
apicomplexan parasites
Nature 451, 959–963 (2008)
In Fig. 2c of this Article, the GenBank accession number DQ174732
was incorrectly cited. The correct accession number is DQ174731
(Chromera velia).
ERRATUM
doi:10.1038/nature06872
Hax1-mediated processing of HtrA2 by Parl
allows survival of lymphocytes and neurons
Jyh-Rong Chao, Evan Parganas, Kelli Boyd, Cheol Yi Hong,
Joseph T. Opferman & James N. Ihle
J. D. Thompson, B. M. Zwickl, A. M. Jayich, Florian Marquardt,
S. M. Girvin & J. G. E. Harris
Nature 452, 72–72 (2008)
In the print and HTML versions of this Letter, Fig. 2b was printed
incorrectly. The PDF version published online is correct. The corrected Fig. 2b is shown below.
b
102
Laser detuning (GHz)
Robert B. Moore, Miroslav Obornı́k, Jan Janouškovec,
Tomáš Chrudimský, Marie Vancová, David H. Green,
Simon W. Wright, Noel W. Davies, Christopher J. S. Bolch,
Kirsten Heimann, Jan Šlapeta, Ove Hoegh-Guldberg,
John M. Logsdon Jr & Dee A. Carter
3.0
2.0
101
1.0
100
0.0
Nature 452, 98–102 (2008)
In Fig. 1a of this Letter, the light blue line was incorrectly labelled
as Hax1/Bak DKO, n 5 13. The light blue line should be labelled
Hax1/Bax DKO, n 5 13.
900
©2008 Nature Publishing Group
0
400
800
Membrane displacement (nm)
1,200