The JapaneseSocietyJapanese Society forforPlant Systematics

ISSNl346-7565 Acta Phytotax, Geobot.56 (l):11-20(2005)

Invited article

"" Origin andEvolutionof as Deduced fromGenome Information

HISAYOSHI NOZAKI

Department ofBiologicat Seiences, Gradttate Schoot ofScience, qf' 7bk}'o, Hongo, Bunkyo-ku, 7bkyo 113-O033, JapanUhiversity

Phylogenetic re]ationships between three lineages of the primary photosynthetic (, green plants and glaucophytes) seemed to remain unresolved because previous nuclear multigene phylogenies used the incomplete red algal gene sequences. Recently, we canied out phylogenetic analy- ses based on a 1 525-amino-acid sequence of four concatenated nuclear genes from various lineages of only mitochondria-containing eukaryotes, using complete genome sequences from the red alga C}'anidioschyzon tnerolae. This study resolved two large monophyletic greups (groups A and B) and the basal group (Ameebozoa), GrQup A corresponded to the Opisthokonta (Metazoa and Fungi), where- as group B included various primury and secondary plastid-centaining lineages (euglenoids, het-

erokonts, and apicomplexans), Ciliophora, , and Heterolobosea. The rod aLgae represented the most basal lineage within group B. Sincc the single event of the plastid primary endosymbiosis was strongly suggested by other data, it was considered that the primary plastid endosymbiosis likely eccurred once in the common ancestor of group B, and the primary plastids were subsequently lost in the ancestor(s) of organisms which now ]ack primary plastids within group B. A new concept of "Plantae" was proposed for photetrophic and nonphototrophic organisms belonging to group B, on the basis of the common history of the primary plastid endosymbiosis.

nuclear endosymbiosis,secondary endesym- Key words: evelution , genes,phylogeny,plastids,primary biosis

"primary Problems in previous nuclear multi- plants, glaucophytes and red algae are eukaryotes", whose may gene phylogeny of the primary photo- photosynthetic plastids have originated directly from a cyanobacterium- synthetic eukaryotes "primary like ancestor via endosymbiosis" (e,g,, The origin and diversity of plastids (chloroplasts) in Bhattacharya & Medlin 1995, Delwiche 1999,

eukaryotic cells can be atuibuted to two types of McFadden 2001, Cavalier-Smith 2002a). By con-

endosymbiotic events: primary endosymbiosis, and trast, the plastids of other lineages of eukaryotic secondary or tertiary endosymbiosis. The green phototrophs appear to be the result of secondary

This article is formed frQm the presentation as one of contributions for the International Symposium 2004,Asian Plant - Diversity and Systernatics, held at Sakura, Chiba, Japan on July 29 August 2, 2004.

NII-Electronic Library Service The JapaneseSocietyJapanese Society for Plant Systematics

12 APG ivbl, 56

or tertiary endosymbiotic events (involving a pho- strated the strong monophyly of red and green totrophic and a host cell) because they are plants based on 13 nuclear genes, but they used

surrounded by three or four bounding membranes, oomycete beta tubulin sequences and two cryp-

and the endosymbiotic remnant of the phetosyn- tomonad nucleomorph (highly reduced red algal thetic eukaryotic nucleus, called the nucleomorph, nucleus after the plastid secondary endosymbio-

may be recognized between the bounding mem- sis) sequences for the red aigal OTU, Therefbre,

branes (e.g.,Delwiche ]999,McFadden 2001, nuclear gene sequences from free-living red algae, Cavalier-Smith 2002a, Ybon et al. 2002). Cavalier- especially from the Cyanidiophyceae, were needed

Smith (1981, 2002b) classified only the primary to reso]ve reliable phylogenetic positions of the "Plantae'". photosynthetic eukaryotes as the three groups of the primary photosynthetic eukary- All of the plastids in eukaryotes can be considered otes. to be the preduct of a single primary endosymbiosis, basedon the phylogenetic analyses ofplastid-cod- Macrophylogeny using nuclear gene ing genes and the similarity of the plastid genome sequences obtained from the genome organization (e,g,, Morden et al. 1992, Nelissen et project of the red alga Cyanidioscltyzon al. 1995, Bhattacharya & Med]in 1995) and the

conserved mosaic origin of Calvin cycle enzymes in Cemplete sequences of all of the three genomes, the red alga (lyanidioscdyzon and green plants (Matsu- mitochondrial (Ohta et aL 1998), plastid (Ohta et al.

zaki et at. 2004), 2003) and nuclear (Matsuzaki et al. 2004) genomes, three Recently, phylogenetic studies of con- from Cly,anidiosch),zon merolae (Cyanidiophyceae)

catenated amino acid sequences of mu]tiple nuclear were deterrnined for the first time in eukaryotic

genes were carTied out (Moreira et al, 2000, Baldauf algae. Nozaki et aL (2003a) thus used complete et al. 2000, Bapteste et at. 2002), However, these sequences of the nuclear genes from C. merolae studies included only a single red algal OTU main- for deducing the natural phylogenetic relationships ly derivedfrom Porphyra. Although the red algae between the three primary photosynthetic eukary- were traditionally assigned to the single class otes. The alignment of four nuclear genes used by Rhodophyceae comprised of two subclasses, the Baldauf et al. (2000) was used, but nucleomorph

Bangiophycidae (includin.u Potph.yra and C>'ani- sequences and amitochondrial sequences were dioschyzon)and the Florideophycidae (e. g. Bold & excluded because these highly divergent gene recent Wynne 19g5), molecular phylogenetic analy- sequences seem te exhibit unusual substitutions, ses demonstrated that the Bangiophycidae are para- which can cause long-branch attraction or unnatur- phyletic, and the red algae are composed of two sis- al phylogenetic resolution (see Van de Peer et at.

ter clades (e,g., Ciniglia et at, 2004), which can be 1996, Stiller et al. 2001). Therefore, only mito- assigned to the Rhodophyceae (including Perphyra ehondria-containing eukaryotes were ana]yzed and Florideophyceae) and Cyanidophyceae (includ-(Nozaki et aL 2003a). ing Cyanidioschyzon and other acid hot spring red Since it was generally considered that the ami-

algae). Baldauf et al. (2000) used four nuclear tochondrial eukaryotes represent the most basal genes of a 1arge number of OTUs from various eukaryotes (see Cavalier-Smith 1998) (Fig. 1), eukaryotes. However, the phylogenetic position exclusion of such organisms from eukaryotic macro-

of the red alga was ambiguous, possibly because phylogenies seemed to result in dithculty for des-

only a single OTU was analyzed and its sequences ignating the outgroup. In order to resolve basal

were incomplete. Moreira et al. (2000) demon- mitochondria-centaining eukaryotes, however,

NII-Electronic Library Service The JapaneseSocietyJapanese Society for Plant Systematics

"plants" April 2005 NOZAKI: Origin and evolution of 13

r Secondary phototrophs tt/

FIG. 1. Diagrams of plastid and mitochondriaE endosymbioses and evo]ution of eukaryotes (based on Cavalier-Smith 1998), N, nuc]e- us; m, mitochondrien.

Nozaki et al. (2003a) canied out the paralogous from 40 mitochondria-containing organisms with

comparison of the combined data set from alpha- those of reversibly concatenated alpha- and beta-

and beta-tubulin sequences. The alpha- and beta- tubulin genes from the same 40 organisms. The tubuiin genes may have originated from gene dupli- alignment was carried out according to McKean

cation, after the origin of eukaryotes (Edlind et at. et aL (2001). After removing the gaps, 560 amino 1996, Keeling & Doolittle 1 996). Therefore, basal acids from 80 OTUs, in total, were used fbr phylo- eukaryotic organisms can be deduced from a phy- genetic analyses (Nozaki et al. 2003a). Figure 2 logenetic comparison of these two genes Csee Iwabe shows the phylogenetic tree constructed using the et al. 1989). In erder to increase the phylogenetic concatenated amino acid sequences of the alpha- and information, Nozaki et at, (2003a) aligned con- beta-tubulin genes, [[iwo identical subtrees are the- catenated sequences of these two paralogous genes oretically resolved. High bootstrap values resolyed

NII-Electronic Library Service The JapaneseSocietyJapanese Society for Plant Systematics

14 APG Vbl.56

Hemo Danio 9971 :t;sMso:IZila thenorhabditis S6 62 Histriculus iVeurospora stndidb ccharenryces * 86 " Sbhizosaccharompees 6 Ps'le#f,m.oewtistum *

PhaeoRoant:iiZSscltyzon eae Red algae Arabidopsis 4(796 veagaenlarrEpdomonas Yblvex 56- ptosporidium 53{-) de pfbsmS}IIum Eimeria .7bpX lalasma a-tueMilin B-tubulin t denuis m m rmophila . meetum 70 8185 eizxep es A9,X.Y,i･,richidae Mffglat.e."t.'" lee{loe)94 7fi(.) Lelshmania

lppanosomabrucgicruu pig,sarum-itmpanosoma 84(99) D.c-fe:$s:iae'z,. Cellular s]ime molds 99 Acytostelium Hbmo Danio

gg gg S9.M,em ila 7bethothenorhabditis

86 e4 IVle"rospera Htstricut ttskecharofiij,ees Chndide S6 68 Pneumt ± :g/Z/utttZOSaCCharontyces Phaeop -Red bygn zon algae Arahidurp SISwr.e,a,fa,Schizop 92-6 9z/:acalaaydbmen"s 52 Fbtvox

PlasmM mtOsporidium su Eimeria lbxoplasma B-tubulin a-tufutiei:a Cbipvda . m t 7e 82 !ll.lz'`.for:'eeM,/f/t.ta 85 E otesO richidae

7 .)ilS!glena de !}l&1'."."re,M.".b.r.".C:ef,' Acrasis fVlaegtaeria --10changes Pijysarum 2 9999 ttSKzti-.eLi,ulynti'..Cel]ular s]ime molds Acytostetiumm

FiG. 2. 0ne of the four most parsimonious tiees ofconcatenated paralogous genes (alpha- and beta-tubulin genes) from 40 mitochonchia- containing organisms based on the unamblguously aligned 560 amino acids, with reversibly concatenated alpha- and beta-tubu- lin genes from the same 40 organisms designated as the eutgroup. Numbers without and with parentheses abeve branches are the beotstrap values (SO% or more) based on 1OOO replications of the full heuristic MP analysis and the neighborjoining method, respec- tively. Branches resolved with 50% er more QPS values by quartet puzzling-maximum likelihood calculation, Asterisks indicate branches not supported by SO% or more boetstrapl quartct puzzling support (QPS) values of the three phylogenetic methods. BootstrapfQPS values supporting distul branches are not shown. (Based on Nozaki et al. (2003a); reproduced by permission of Springer-Verlag New Ybrk Inc,),

NII-Electronic Library Service The JapaneseSocietyJapanese Society for Plant Systematics

"plants" Apri1 2005 NOZABCI: Origin and evolution of 15

that the most basal position of the clade was held by Hetero]obosea, where the red algae represent the three cellular slime molds, Therefore, the cellular most basal group and the glaucophyte C.vanophora slime molds were designated as the outgroup in is the secondary basal lineage. The green plants our phylogenetic analyses of fbur nuclear genes are positioned distally within group B (Fig. 3). (Nozaki et aL 2003a). These phylogenetic positions are consistent with Recently, Cavalier-Smith (2002b) and Stech- the fact that the g]aucophytes and red algae have mann & Cavalier-Smith (2002) suggested that the plastids with primitive features, such as phycobil- represent the most basal eukaryotic lisomes, common to the cyanobacteria (e.g., Bold & lineage, based on the diversification of the micro- W}rnne 1985, South & Whittick 1987), A]though the

tubu]ar cytoskeleton and/or presence/absence of group B was not robustly resolved (Fig. 3), the dihydrofolate reductase-thymidylate synthase monophyly of this group is supported by the pres- (DHFR-TS) gene fusion. TherefoTe, the cellular ence of DHFR-TS gene fusion (Stechmann &

slime molds appear to be one of the most basal CavalieFSmith 2002, for red algae, see the sequence

eukaryotic organisms and are appropriate as the data of Matsuzaki et al. 2004).

outgroup in phylogenetic analyses of mitochon- dria-containing organisms, Although Stechmann & A new scenario of plastid endosymbio- "Plantae" Cavalier-Smith (2003) and Cavalier-Smith (2003) sis and new concept of the

very recently suggested that the Opisthokonta

(Metazoa and Fungi) and Amoebozoa represent a The phylogenetic results by Nozaki et al, (2003a) monophyletic group (unikonts), based on the unique also suggested that the plastid primary endosym- fusion of three genes in the pyrimidine biosynthet- biosis likely occurred once in the common ancestor ic cluster (the CAD complex: carbamoyl-phosphate of group B, and primary plastids were subsequent- synthetase II, aspartate carbamoyltransferase, and ly lost in the ancestors of the primary plastid lacking dihydroorotase), this gene fusion is found in the erganisms belonging to this group (Fig. 4), Thus, nuclear genome of the red a]ga CyanidioschyzonDiscicristata, Heterokonta and Alveolata might merolae (Matsuzaki et al. 2004, Nozaki et at. 2005). haye experienced the primary endosymbiQsis. [Ib resolve the reliable phylogenetic position of are characterized by having disk-

the red algae within the eukaryotic organisms, shaped mitochondria cristae, and include

Nozaki et al. (2003a) performed phylogenetic analy- Heterolobosea, Kinetoplastida, and the Eugleno- ses of various eukaryotic, mitochondria-containing phyceae which contain the secondary plastids organisms based on a 1525-amino-acid sequence ef (Cavalier-Smith 2002b), Alveolata include fbur concatenated nuclear genes (actin, elongation Cilliophora and two secondary plastid-containing factor-lalpha, alpha-tubulin and beta-tubulin). The greups, namely, and , analyses resolved the presence of two Large mono- (Cayalier-Smith 2002b). Although the three groups phyletic groups (groups A and B) and the basal of the secondary phototrophs (Haptophyceae, lineage, Amoebozoa (tme and cellular slime molds) and Chlorarchniophyceae) were not

(Nozaki et al. 2003a) (Fig. 3), Group A corre- analyzed by Nozaki et at, (2003a), recent studies of sponded to the Opisthekonta (Metazoa and Fungi), the plastid-targeted glyceraldehyde-3-phosphate whereas group B included various primary and sec- dehydrogenase genes demonstrated that the sec- ondary plastid-containing ]ineages (red aLgae, green ondary plastids of the Haptophyceae, Cryptophy- plants, glaucophytes, euglenoids, , and ceae, Dinophyceae, Apicomplexa and Heterokonta

apicomplexans), Ciliophora, Kinetoplastida, and have the single endosymbiotic origin (Harper &

NII-Electronic Library Service TheTheJapaneseSociety Japanese Society for PlantPlantSystematics Systematics

16 APG Vbl. 56

([}roup A

B

Amoehozoa

AgpTes

-50 changes

FIG. 3. 0ne of the two most parsimonious tree (with tree length of 5221 and consistency index of U.5417) based on 1525 amino acid sequences from the four nuclear genes (actin, elongation facter- lalpha, alphu-tubulin and beta-tubulin) of 53 OTUs representing a wide-range of mitochondria-containing eukaryotic tuxa. Branch lengths are proportional te numbers of amino acid substitutions, which are indicated by the scale bar beLow the tree. Numbers above branches are the bootstrap va]ues (50% or more) based on 1OOO replications of the fuIl heuristie analysis (with simple addition sequence). Single and double asterisks indicate the primary and sec- ondary plastids, respectively. (Based on Nozaki et al. (2003u); reproduccd by permission of Springer-Verlag New York Inc.).

NII-Electronic Library Service The JapaneseSocietyJapanese Society for Plant Systematics

"plants" April 2005 NOZAKI: Origin and evolution of 17

Keeling 2003). Therefore, almost all of the sec- totrophy occurred in the comrnon ancestor of the

ondary plastids appear to have evolved after the monophyletic plastid-containing group (Euglenales) plastid primary endosymbiosis, based on the phy- distally positioned within the Euglenophyceae logenetic study by Nozaki et al, (2003a) (Figs, 3, 4), (Montegut-Felkner & Triemer 1997, Preisfeld et

Therefbre, establishment of the secondary endosym- aL 2000; MUIIner et al. 2001), and the Hetero-

biosis may be based on the experience of the plastid lobosea are positioned outside the clade composed

primary endosymbiosis, The genes that had con- of Euglenophyceae and Kinetoplastida (Baldauf et

tributed to the primary endosymbiosis might have al. 2000, Nozaki et al. 2003a) (Figs. 3, 4). In addi-

also contributed to the secondary endosymbiosis, tion, the cladistic analysis of plastid gene losses Andersson & Roger (2002) demonstrated that suggested the relatively recent acquisition of the the 6-phosphogluconate dehydrogenase (gndi gene secondary plastid of Eugtena (after the divergence with cyanebacterial affinity are present in the nuclear of Chlorophyceae and Ti:ebouxiophy-ceae) (Nozaki genomes of photosynthetic eukaryotes as well as of et al, 2003b). Therefore, the plastid secondary plastid-lacking organisms of Heterokonta and endosymbiosis can hardly be considered before the Heterolobosea, and these genes foim a monophyletic divetgence of Euglenophyceae and Kinetoplastida or group that is sister to the cyanobacterial clade. Heterolobosea, and the cyanobacterial or plant-like

Therefore, two alternative hypotheses were sug- genes found in Heterolobosea (Andersson & Roger gested. First, the gnd genes might have intreduced 2002) and Kinetoplastida (Hannaert et al. 2003)

to the nucleus from the cyanobacteria during the are possibly derived from the ancient primary p]as- t`ancient" primary endosymbiosis. Second, the sec- tid endosymbiosis suggested by Nozaki et al. ondary endosymbiosis might have mediated the (2003a) (Fig. 4). Thus, Nozaki et at. (2003a) pro- "Plantae" gene transfer ef gnd. The phylogenetic results by posed a new concept of for the large Nozaki et al. (2003a) are consistent with the first monophyletic group resolved (group B, Fig, 3), hypothesis and these cyanobacterial genes in the based on the common history of the plastid prima- "relics" nuclear genome can be considered of the ry endesymbiotic eyent (Fig. 4), The Planatae plastid primary endosymbiosis (Fig. 4). include primary plastid-containing phototrophs and Very recently, several cyanobacterial or plant- eukaryotes that possibly contain cyanobaterial genes like genes were found in the plastid-lacking acquired in the primary endosyrnbiosis, Since the

"Plantae" Kinetoplastida by Hannaert et al. (2003). Since sensu Cavalier-Smith (1981, 2002b) (only the Euglenophyceae have secondary plastids and are the primary plastid-contajning eukaryetes) are appar- "P]antae" closely related to the Kinetoplastida, Hannaert et al, ently paraphyletic, the concept of of (2003) discussed that a common ancestor of both Nozaki et at. (2003a) is more natural and based on Euglenophyceae and Kinetoplastida already ac- the important evolutionary event (plastid primary quired the secondary plastids that gave rise to the endosymbiosis) during the eukaryotic evolution. plant-like genes in the Kinetoplastida nuclear The members of the Plantae emended by Nozaki et genome. Furtherrnore, Cavalier-Smith (2003) sug- al. (2003a) are very similar to those of the Bikonta gested the single, very ancient secondary endosym- () recently proposed by Stechmann & biosis of green alga befbre diverge"ce of Disci- Cavalier-Smith (2002, 2003) and Cavalier-Smith cristata and (including the secondary pho- (2003) (Fig. 5), who classified the eukaryotes into tosynthetic eukaryotes Chlorarachniophyta) (Fig. the Amoebozoa, Opisthokonta, and Bikonta, on the

5). However, phylogenetic analyses of various eug- basis of cell morphology and synapomorphic lenoid taxa suggested that the evolution of pho- changes in gene organization (insertion, gene fusion,

NII-Electronic Library Service The JapaneseSocietyJapanese Society forforPlantSystematics Plant Systematics

18 APG M)1. 56

Plantae

tt

t*a

Bikonts

** Euglenophyceae

Kinetopla$tida

Heterolobesea

* Red Algae

* Glaucophyta

** eterokontophyta

** picomplexa

liophora Fig. 5

FiGs. 4, 5. TXMo Tecent hypotheses of the origin and evolution of plastids. Single and doub]e asterisks indicate the primary and secondary plastids, respectively. 4: Based on Nozaki et al. (2003a). 5: Based on Cayalier-Smith (2003).

NII-Electronic Library Service The JapaneseSocietyJapanese Society for Plant Systematics

'`plants" Apri] 2e05 NOZAKI: Origjn and evolution of 19

etc.) (Fig, 5). However, eyolutionary events of the R64, , 2002b. The origin of eukaryotes and primary plastids after the primary endosymbiosis are phagotrophic phylogenetic classification of . Int. J, Syst. essentially different between the Plantae (Fig. 4) and Evol. Microbiol. 52: 297-354. Bikonta (Fig. 5), In the Bikonta, the plastid prima- . 2003, The excavate protozoan phyla Metamonada ry endosymbiosis have been experienced in the Grasse emend. (, Parabasalia, ancestor of only three of the the groups primary Carpediernona$, EQpharyngia) and Leukozoa emend. photosynthetic eukaryotes because the three groups (Jakobea, ): their evoLutionary atiinities and new higher taxa, Int. J. Syst. Evol. Microbiol. are still believed to be monophyletic (Fig. 5). 53:1741-1758.

Ciniglia, C., H. S. Ybon, A, Pollio, G, Pinto & D, This work was supported by Grant-in-Aid for Creative Bhattacharya. 2004, Hidden biediversity of the Scientific Research (No. 16GS0304) and by Grant-in- "Genome extremophilic Cyanidiales red algae. Mol. Ecol, l3: Aid for Scientific Research on Priority fM/eas (c) 1827-1838. Biology" (No. 1320611) from the Ministry of Education, Delwiche, C, F, 1 999, Tracing the thread of plastid diver- Cu]ture, Sperts, Science and TechnolQgy, Japan. sity through thetapestry of life. Am. Nat. 154: 164- 177, References Edlind, T. D., J. Li, G. S. Visvesvara, M. H. Ivhdkin, G. L. McLaughlin & S. K. Katiyar. 1996. Phylogenetic Reger. 2002. A cyanobacterial Andersson,J.O.& A. J. analysis of beta-tubulin sequences from amitochon- in nonphotosynthetic -An early chloro- gene protests drial protozoa. Mol. Phylogenet. Evol. 5: 359-367. plast acquisition in Eukaryotes? Curr. Biol. 12: 115- Hannaert, VL, E. Saavedra, F, Duffieux, J. R Szikora, D, J. 119. Rigden, R A. M. Michels & F. R. Opperdoes. 2003. Buldauf, S. L., A, J, Roger, I. Wenk-Siefert & W. F. Plant-like traits associated with metabolism of

Doolittle. 2000. A kingdom-level of phylegeny 7}lypanosoma parasites. Proc. Natl. Acad. Sci, USA eukaryotes based on combined protein data. Science 100: 1067-1071.

290:972-977. Harper, J. T. & R J. Keeling, 2003. Nucleus-encodcd, plas- A, Lee, D. M Moore, C. W, Bapteste, E., H, Brinkmann, J, tid-targeted glyceraldehyde-3-phosphate dehydro- R Gordon, L. Durufl6. T. Gaasterland, P, Sensen, genase CGAPDH) indicates a single origin for Lopez, M. MUIIer & H, Philippe. 2002. The analysis Chromalveolate plastids. Mol. Biol Evol 20: 1730- of 1OO genes supports the grouping of three highly 1735,

divergent amoebae: Dictyostelium, Entamoeba, and Iwabe, N., K. Kuma, M. Hasegawa, S. Osawa & T.

Mastigamoeba. Proc, Natl, Acad. Sci. USA 99: Miyata. 1989. Evolutionary relationship of archae- 1414-1419, bacteria, eubacteria, and eukaryotes inferred from Bhattacharya, D. & L. Medlin. 1995. The phylogcny of phylogenetic trees of duplicated genes. Proc. Natl, plastids: A review based on comparisens of small Acad. Sci, USA 86: 9355-93S9.

subunit ribosomal RNA coding regions. J, Phycol. Keeling, R J. & W, F, Doolittle. 1996. Alpha-tubulin 31:489-498. from early-diverging eukaryotic lineages and the J. M. Wynne. 198S. Introduction to the Bold,H, C,& evolutien of the tubulin family. Mol, Biol. Evol. 13: Algae, 2nd edn. Prentice-Hall. Inc., Englewood 1297-1305.

Cliffs, New Jersey, Matsuzaki, M., O. Misumi, T. Shin-i, S. Maruyuma, M.

Cavalier-Smith, T 1981. Eukaryote kingdorns, seven or 1lakahara, S. Y: Miyagishima, T. Mori, K. Nishida, E nine?BioSystems 14: 461-481. Yagisawa, K. Nishida, YL Ybshida, Yl Nishimura, S, , 1998. Nemomonada and the erigin of and Nakao, T, Kobayashi, YL Momoyama, T, Higashi- fungi. In: Coombs, G. H. & K. Vickerman. (eds.) yama, A, Minoda, M, Sano, H. Nomoto, K. Oishi, H. Eyolutienary Relationships among Pretozoa., pp. Hayashi, F. Ohta, S. Nishizaka, S. Haga, S. Miura, T 375-407, Kluwer Academic Publishers, Dordrecht, Morishita, Y. Kabeya, K. [[brasawa, Yl Suzuki, Y/ . 2002a. ChloropLast evolution: Secondary symbio- Ishii, S. Asakawa, H. [Ihkano, N, Ohta, H. Kuroiwa, multiple ]osses.Curr. Biol. 12: R62- genesis and K. Tanaka, N, Shimlzu, S. Sugano, N. Sato, H.

NII-Electronic Library Service The JapaneseSocietyJapanese Society for Plant Systematics

20 APG ivbl. 56

Nozaki, N. Ogasawara, YL Kohara & T. Kuroiwa, Evol. 56: 485-497.

sequence of ultrasmall unicellular N. 2004.Genome the , Ohta,M. Matsuzaki,O. Misumi & T. Kuroiwa. red alga C>,anidioschyzon merolae 10D. Nature 428: 2003b. Phylogeny of plastids based en cladistic 653-657, analysis of gene loss inferred from complete plastid McFadden, G. I.2001 .Primary and secondary endosym- genome sequences, J, Mol. Evel, 57: 377-382. and the origin biosis of plastids. J. Phycol, 37: 951- Ohta, N., M, Matsuzaki, O, Misumi, S. Miyagishima, rlhnaka, 959. H. Nozaki, K. T. Shin-i, Y Kohara & T. McKean, R G,, S, Vliughan & K. Gull. 2oo1, The extend- Kuroiwa. 2003, Complete sequence and analysis of

ed tubulin superfamily. J Cel] Sci114:2723-2733, the plastid geneme of the unicellular red alga Montegut-Felkner, A. E. & R. E. Triemer, 1997. (]:y'anidioschyzon metviae. DNA Res, 10: 67-77.

Phylogenetic relationships of selected euglenoid N. and organi- , Sato& T,Kuroiwa.1998.Structure genera based on morphelogical and molecular data. zation of the mitochondrial genome of the unicellu- J. Phycol. 33: 512-519 1ar red alga Cb,anidiosch}rzon merolae deduced from Morden, C. W., C. F. De]wiche, M. Kuhsel & J.D. the complete nucleotide sequence. Nucleic Acids Palmer. 1992. Gene phylogenies and the endosyrn- Res. 26: S190-5198. biotic origin of p]astids. BioSystems 28: 75-90. Preisfeld, A,, S. Berger, I. Busse, S. LMer & H, G. Moreira, D., H. Le Guyader & H. Philippe, 2000. Tlie ori- Ruppel. 2000. Phylogenetic analyses of various eug- gin of red algae and the evolution of chloroplasts, leneid taxa () based on 18S rDNA Nature 405: 69-72, sequence data. J. Phycol. 36i 220-226. MUIIner, A. N., D. G, Angeler, R. Samuel, E, Wl Linton & South, G. R. & A. Whittick. 1987. Introduction to R. E. Triemer. 2001. Phylogenetic analysis of Phycology. Blackwell Sci. Pub., Oxford. phagotrophic, phototrophic and osmotrophic eugle- Stechmann, A. & T, Cavalier-Smith. 2002. Rooting the

noids by using the nuclear 1 rDNA 8S sequence, Int. eukaryote tree by using a derived gene fusion. J, Syst, Evol. Micr. 51: 783-791 Science 297: 89-91. Nelissen, B., Y. Van de Peer, A. Wilmotte & R, De & , 2003, The root of the eukaryote tree pin- Wachter. 1995. An early origin of plastids within pointed. Curr ,Biol. 13: R665-R666, the cyanobacterial divergence is suggested by evo- Stiller, J, W., J. Riley & B. D, Hall. 2001, Are red algae lutionary trees based Qn complete 16S rRNA plants? A critical evaluation of three key molecular sequences. Mol Biol Evol 12: 1166-1173. data sets. J. Mol, EvoL. 52: 527-539.

Nozaki, H,, M, Matsuzaki, O. Misumi, H. Kuroiwa, T, Van de Peer, IL, S. A. Rensing, U, G. Maier & R, De Higashiyama & T. Kuroiwa, (in press) Phylogenetic Wachter, 1996, Substitution rate calibration ef small implications of the CAD complex from the primitive subunit ribosomal RNA identifies chlorarachnio-

red alga C),anidioschyzon merolae (Cyanidiales, phyte endosymbionts as remnants of green algae. Rhodophyta).J.Phycol.41. Proc. Natl. Acad. Sci. USA 93: 7732-7736.

, M. Matsuzaki,M. Takahara,O, Misumi,H. Kuroiwa, Ybon, H. S., J. D. Hackett & D, Bhattacharya. 2002. A M. Hasegawa, T, Shin-i, Yl Kohara, N. Ogasawara & single origin of the peridinin- and fucoxanthin-con- T, Kuroiwa. 2003a. The phylogenetic position of taining plastids in dinofiagellates through tertiary red a]gae revealed by multiple nuclear genes from endosymbiosis. Proc. Natl, Acad, Sci. USA 99: mitochondria-containing eukaryotes and an alterria- l1724-11729. tive hypothesis on the origin of p]astids. J. Mol,

Received July 26, 2004;accepted December J4, 2004

NII-Electronic Library Service