INVITED ARTICLE

Genome analysis and its significance in four unicellular algae,Cyanidioshyzon merolae, Ostreococcus tauri, Chlamydomonasreinhardtii, and Thalassiosira pseudonana

Osami Misumi Æ Yamato Yoshida Æ Keiji Nishida Æ Takayuki Fujiwara ÆTakayuki Sakajiri Æ Syunsuke Hirooka Æ Yoshiki Nishimura Æ Tsuneyoshi Kuroiwa

Received: 5 October 2007 / Accepted: 30 October 2007 / Published online: 12 December 2007

� The Botanical Society of Japan and Springer 2007

Abstract Algae play a more important role than land

plants in the maintenance of the global environment and

productivity. Progress in genome analyses of these organ-

isms means that we can now obtain information on algal

genomes, global annotation and gene expression. The full

genome information for several algae has already been

analyzed. Whole genomes of the red alga Cyanidioshyzon

merolae, the green algae Ostreococcus tauri and Chla-

mydomonas reinhardtii, and the diatom Thalassiosira

pseudonana have been sequenced. Genome composition

and the features of cells among the four algae were com-

pared. Each alga maintains basic genes as photosynthetic

eukaryotes and possesses additional gene groups to repre-

sent their particular characteristics. This review discusses

and introduces the latest research that makes the best use of

the particular features of each organism and the signifi-

cance of genome analysis to study biological phenomena.

In particular, examples of post-genome studies of organelle

multiplication in C. merolae based on analyzed genome

information are presented.

Keywords Algae � Genome � Organelle � Metabolism �Photosynthetic organisms

Introduction

Algae are a highly diverse group of organisms that live in a

variety of environments, such as in oceans, in fresh water,

in the soil, on ice, on rock, and so on. This characteristic

makes algae very suitable for studies concerning the

adaptation of organisms to different environments, and it

provides the possibility of finding novel genes related to

different environmental tolerance characteristics. Cyanid-

ioshyzon merolae is an unicellular red alga which lives in

extreme environments, such as those at high temperatures

or that are strongly acidic (De Luca et al 1978). In addition,

algae are highly morphologically diverse. Species vary

from single-celled to multiple-celled. They vary in size too;

for example, cells of the picoplankton ex. Ostreococcus

tauri are *1 lm in diameter (Derelle et al. 2002), whilst

Ecklonia cava (Laminariaceae) may reach a length of

more than 2 m. In addition they vary in terms of their

growth habits (for example, volvocales species form col-

onies) or in their physical structure (for example, many

haptophytes have an exoskeleton of calcareous plates

called coccoliths). Thus algae are suitable for studies of

cell differentiation.

One of the most important topics in algal research is

photosynthesis. The mechanism of photosynthesis in the

chloroplast of green algae is basically similar to that of

land plants. Therefore, many of the phenomena analyzed

O. Misumi � K. Nishida � T. Fujiwara � T. Sakajiri �S. Hirooka � T. Kuroiwa

Department of Life Science, Graduate School of Science,

Rikkyo University, Tokyo 171-8501, Japan

Y. Yoshida

Department of Integrated Biosciences, Graduate School

of Frontier Sciences, The University of Tokyo,

Chiba 277-8562, Japan

Y. Nishimura

Institute of Molecular and Cellular Biosciences,

The University of Tokyo, Tokyo 113-0032, Japan

T. Kuroiwa (&)

Research Information Center for Extremophile,

Rikkyo University, 3-34-1 Nishiikebukuro,

Toshima-ku, Tokyo 171-8501, Japan

e-mail: tsune@rikkyo.ne.jp

123

J Plant Res (2008) 121:3–17

DOI 10.1007/s10265-007-0133-9

using algae can be applied to higher plants. For example,

the heterotrophic ability of Chlamydomonas to utilize

alternative carbon sources as nutrition allows photosyn-

thetic mutants to persist (Harris 1989). Algae have

contributed considerably to research in this field. The

biomass resources of algae in the ocean are of immense

importance in the global environment. Algae have also

contributed to research into a variety of other phenomena

in cell biology. Studies of eukaryote sexual reproduction

and life cycles have often been investigated using algae.

In addition, research into flagellar movement (Dutcher

1995) or organelle multiplication, applicable to eukary-

otic organisms in general, has been developed using

unicellular algae with simple morphologies. Analyzing

algal genomes provides important information for

research into not only the simple acquisition of nucleo-

tide sequences, but also the physiology, environmental

adaptation mechanisms, morphogenesis and evolution of

organisms (especially the origin of photosynthetic

organisms, and their evolution into land plants). This

short review covers four algae, C. merolae, O. tauri, C.

reinhardtii and T. pseudonana, the compositions of their

respective algal genomes, and introduces research that

relates to this genome information. In particular we

suggest that Cyanidioschyzon merolae cells, with heat-

stable proteins that are unique among eukaryotes, are

fundamental to future studies of proteomic expression

analysis using microarrays and those in structural

biology.

Outline of sequenced algal genomes

Figure 1 shows the phylogenetic position of each alga on

Nozaki’s phylogenetic tree (Nozaki et al. 2003). C. mer-

olae belongs to the Rhodophyta, which diverged earliest

among photosynthetic organisms. O. tauri and C. rein-

hardtti belong to the green lineage. These algae have a

plastid acquired by primary endosymbiosis of ancestral

cyanobacteria. On the other hand, T. pseudonana has a

plastid acquired by secondary endosymbiosis and belongs

to the Heterokontophyta. Figure 2 shows fluorescent

photomicrographs of each algal cell stained with DAPI.

Blue-white fluorescence in the cells indicates the com-

partments where genomic DNA exists. The chloroplast

DNA of C. merolae is located at the center of the chlo-

roplast, while O. tauri and C. reinhardtii have dispersed

DNA similar to the chloroplasts of the higher plants. The

chloroplast DNA of T. pseudonana exists along the edge

of the chloroplast envelope. One spherical mitochondrion

is contained in the cells in C. merolae and O. tauri.

However, in other species mitochondria have altered

forms and sizes through division or fusion, and such

complex forms are found in C. reinhardtii and

T. pseudonana. Multiple genome DNA molecules are

usually contained in the chloroplast and mitochondria;

photosynthesis and respiration of cells functions through

replication and distribution of this DNA.

airetcaB

atyhpodohR

atyhpocualG

arohpoiliC

axelpmocipA

atyhpotnokoreteH

aesoboloreteH

aditsalpoteniK

aozonelguE

stnalP neerG

ignuF

aozateM

aozobeomA

aeahcrA

Cell nucleus

Mitochondrion

Chloroplast

Oposthokonta

2

3

4

I

II

III

1

Bikonta (Plantae) Amoebazoa

Fig. 1 Phylogenetic positions of Cyanidioschyzon merolae (1),

Ostreococcus tauri (2) Chlamydomonas reinhardtii (3) and Thalass-iosira psudonana (4) on a modified version of Nozaki’s phylogenetic

tree (Nozaki et al. 2003). The points of primary endosymbiosis of

alphaproteobacteria (I), primary endosymbiosis of cyanobacteria (II)and secondary endosymbiosis of red algae are represented. C. merolaebelongs to the Rhodophyta and O. tauri and C. reinhardtti belong to

the green lineage. T. pseudonana belongs to the Heterokontophyta

with secondary endosymbiotic chloroplasts

Fig. 2a–d Fluorescent photomicrographs of C. merolae (a), O. tauri(b), C. reinhardtti (c), and Nitzschia sp. cells (d) after staining with

4,6-diamidino-2-phenylindole (DAPI). The spherical or ovoid-shaped

cell nuclei emit blue-white fluorescence (arrows) and chloroplasts

emit red autofluorescence. The chloroplast nuclei (nucleoids) of C.reinhardtii are scattered in the chloroplast while those of sequenced T.psudonana and Nitzschia sp. are located in a ring on the periphery of

the chloroplast. Scale bar 1 lm

4 J Plant Res (2008) 121:3–17

123

Cyanidioschyzon merolae

A summary of the cellular components of the four algae

with complete genome sequences is shown in Table 1, and

an outline of the genome, cell and organelle structures for

these algae is shown in Table 2. C. merolae was the first

alga to provide a complete genome sequence (Matsuzaki

et al. 2004; http://merolae.biol.s.u-tokyo.ac.jp/). C. merolae

has been very useful as a model organism for studies of the

division and multiplication of cell organelles (Kuroiwa

1998; Kuroiwa et al. 1998, 2006). The genome project of C.

merolae was performed in order to elucidate these mecha-

nisms. C. merolae cells contain a minimal set of organelles

for eukaryotes, and the cells proliferate by an extremely

simple binary division process (Kuroiwa et al. 1994, 1998;

Misumi et al. 2005). Sexual reproduction has not been

recorded, although some genes concerning gamete fusion

and sexual differentiation were found in the genome (Mori

et al. 2006; Nozaki et al. 2006). Recently, the complete cell-

nuclear genome sequences were released (Nozaki et al.

2007). Since the completion of the mitochondrial and

plastid genome sequences, C. meolae has become the first

eukaryote in which all three genome compartments—cell

nucleus, mitochondrion and plastid—have been completely

sequenced (Nozaki et al. 2007). The complete sequence of

C. merolae consists of 16,546,747 nucleotides covering 20

linear chromosomes from telomere to telomere (Table 2).

These 20 linear nuclear chromosomes plus the two circular

organelle DNA molecules comprise the entire genome of

the organism, and contain 16,728,945 base pairs. The

nuclear genome encodes 4,775 protein-coding genes, and

the mitochondrial and plastid genomes encode 34,205

protein-coding genes, respectively. The unique feature of

the genome of C. merolae is that it is simple but that it has

Table 1 General features of four algal genomes

Feature C. merolae O. tauri C. reinhardtii T. pseudonana

Nucleus

No. of chromosomes 20 20 17 24

Genome size (bp) 16,546,747 12,600,000 121,000,000 31,300,000

G + C content (%) 55 58 64a 47

No. of genes 5,335 7,892 15143a 11,390

Mean gene length (bp) 1,551 1,245 1580a 1745

Gene density (bp per gene) 3,102 1,597 7,851a 3,500

Percent coding 44.8 81.6 16.7a 28.8

Genes with introns (%) 0.5 39 92a ND

No. of introns 27 4,730 ND ND

Mean length of intron (bp) 248 126 373a ND

Mean length of exons (bp) 1,540 750 190a ND

No. of tRNA genes 30 174 259a 131

No. of 5S rRNA genes 3 4 3a,b ND

No. of 5.8S, 18S and 28S rRNA units 3 4 3a,b *35

Mitochondrion

Molecule Circular Circular Linear Circular

Genome size (bp) 32,211 44,237 15,758 43,827

G + C content (%) 27.1 38.2 45.2 30.1

No. of protein genes 34 43 8 35

Density (bp per protein genes) 947 1,029 1,970 1,252

Plastid

Molecule Circular Circular Circular Circular

Genome size (bp) 149,987 71,666 203,828 128,814

G + C content (%) 37.6 39.9 34.5 30.7

No. of protein genes 208 61 69 141

Density (bp per protein genes) 721 1,175 2,954 914

Data for O. tauri, C. reinhardtii, T. pseudonana are from Derelle et al. (2006); Palenik et al. (2007); Armbrust et al. (2004), the JGI website

(http://www.jgi.doe.gov/) and the NCBI website (http://www.ncbi.nlm.nih.gov/). ND not determineda These data were obtained from Merchant et al. (2007) after their manuscript was submittedb The number is the outermost copies in tandem arrays on three linkage groups

J Plant Res (2008) 121:3–17 5

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Table 2 Comparison of the cellular components of C. merolae, O. tauri, C. reinhardtii and T. pseudonana

C. merolae O. tauri C. reinhardtii T. pseudonana

Lineage Rhodophyta,

Cyanidiophyceae

Chlorophyta,

Prasinophyceae

Chlorophyta,

Chlorophyceae

Heterokontophyta,

Bacillariophyceae

Cell diameter 1–2 lm \1 lm 5–10 lm 5–10 lm

Cell division Binary fission Binary fission Endospore division Division with frustule

Double-membrane bounded

Nucleus

Chromosome number 20 20 17 24

Ploidy Haploid Haploid (diploid?) Haploid, diploid Haploid, diploid

Genome size 16.5 Mbp 12.6 Mbp 120 Mbp 31.3 Mbp

Telomeric repeat GGGGGGAAT TTTAGGG TTTTAGGG TTAGGG

Nucleolus + + + +

Chromatin, dispersed + - + +

Chromatin, condensed + - + +

Metaphase chromosomes Dispersed ND Condensed Condensed

Mitotic spindle with microtubule Internuclear Not observed Internuclear Internuclear

Meiosis Unclear Unclear + +

Mitochondria

Origin Primary endosymbiosis Primary endosymbiosis Primary endosymbiosis Primary endosymbiosis

Number per cell 1 1 One-many Many

Nucleoids Centrally located Centrally located Centrally located Centrally located

Shape Erythrocyte-shaped Ovoid-shaped Oval, elongated, branching Oval, elongated, branching

Dynamics Binary division Binary division Division, fusion Division, fusion

Plastid

Origin Primary endosymbiosis Primary endosymbiosis Primary endosymbiosis Secondary endosymbiosis

Number per cell 1 1 1 Many

Nucleoids Centrally located Scattered Scattered Ring

Shape Spherical Ovoid Cup shape Oval

Thylakoid Single layer Multilayer with grana Multilayer with grana Triple layer

Pyrenoid No No 1-few 1

Eyespot No No 2–4 layers No

Dynamics Binary division Binary division Binary division Binary division

Starch granules Cytoplasm Stroma Stroma Cytoplasm

Single membrane bounded

ER + + + +

Golgi apparatus 1 1 10* 10*

Microbody 1 1 A few A few

Lisosome 2–4 Several vesicles Several Several

Contractile vacuole No No 2 No

Cell motility No No Two flagella No

Cell wall No typical wall Cellulosic wall Cellulosic wall Silicified wall

Sexual reproduction Unclear Unclear + (mating type plus, minus) +

Mating structure No No + -

Data for O. tauri, C. reinhardtii, T. pseudonana are from Derelle et al. (2006); Palenik et al. (2007); Henderson et al. (2007); Armbrust et al.

(2004), the JGI website (http://www.jgi.doe.gov/) and our observations

6 J Plant Res (2008) 121:3–17

123

sufficient genes to function as an eukaryote (Misumi et al.

2005). A typical example is that of the ribosomal DNA gene

units. Most eukaryotes have multiple copies of their rDNA

units in tandem, making a nucleolus, but C. merolae has

only three copies of its rDNA units although it makes an

obvious nucleolus (Maruyama et al. 2004). In many species,

histone genes also tend to make repeating clusters found on

each chromosome. C. merolae histone genes are localized

on chromosome 14 and form a small cluster. The five major

histone genes encode two copies of the three core histone

genes (H2A, H2B and H4), three copies of the H3 gene, and

a single copy of the linker-histone H1 gene, respectively

(Nozaki et al. 2007). This is perhaps the simplest compo-

sition of histone genes. Although the encoded genes of

histone are the minimum set, a general chromatin structure

is formed. The sequencing of all chromosomal termini

sequenced has indicated that AATGGGGGG is the telo-

mere repeat sequence in all chromosomal ends of C.

merolae (Nozaki et al. 2007). This telomeric nucleotide

sequence is different from that of typical green plants. This

may be a characteristic peculiar to red algae, and it would be

interesting to determine teleomeric sequences in closely

related alga such as Cyanidium cardalium and Galdieria

suruphuraria. The C. merolae genome contains 26 class I

elements (retrotransposons) and eight class II elements

which constitute only about 0.7% of the whole nuclear

genome. The transcripts of three of the 26 retrotransposons

are contained an intact reverse transcriptase open-reading

frame. A BLASTX search suggested that all 26 retrotrans-

posons were closely related to non-long terminal repeat

retrotransposons. Although LTR retrotransposons are

widely distributed in eukaryotes, there are none in the

C. merolae genome. In contrast, there were 253 copies of

a novel interspersed repetitive element similar to the shrimp

spot syndrome virus. These repetitive elements have an

average size of 3.2 kbp, and are distributed randomly on all

chromosomes, and together comprise about 5% of the

genome (Nozaki et al. 2007).

Ostreococcus tauri

Ostreococcus is a member of the so-called picoplankton

family of marine algae. Their cell size of 1 lm is the

smallest among the eukaryotes. Recently, a detailed three-

dimensional structure of O. tauri, obtained using electron

cryotomography, has been described (Henderson et al.

2007). The alga was found to be composed of one nucleus,

mitochondrion, chloroplast, peroxisome (microbody),

Golgi body, and several vesicles and granules. It belongs to

family Prasinophyceae, which is believed to be the most

primitive species in the green lineage from which all other

green algae and ancestors of land plants descended. O. tauri

also has a small genome size, with 12.6 million base pairs in

the nuclear genome, 20 chromosomes and 7,892 genes

(Derelle et al. 2006; Palenik et al. 2007; Table 2). This alga

has 1.5 times the number of genes of C. merolae. The

mitochondria and plastid genomes of this alga have also

been determined, and have 44,237 and 71,666 base pairs,

respectively (Table 2). On the other hand, the genome size

of O. tauri has been estimated, using cytological fluores-

cence quantity analysis of nuclear DNA, to be larger than

the sequenced size reported. Although there is a possibility

that diploid cells exist, the quantitive analysis showed

20 million base pairs (Fig. 3; Table 3; Kuroiwa et al. 2004).

Therefore, the detailed analysis remains to be resolved. The

genome of the alga was found to be extremely compressed

and the inter-ORF region between the genes was only

197 base pairs on average. It is by far the smallest organism

among the eukaryotes. A comparatively uniform GC con-

tent of 58% occurs across almost the entire genome, but

falls to 54 and 52% for chromosome 19 and for half of

chromosome 2, respectively. In addition, about 80% of the

transposable elements concentrated in these regions also

show abnormality. A genome sequence for O. lucimarinus,

a closely related species of O. tauri, was completed recently

(Palenik et al. 2007). O. lucimarinus has 13.2 million base

pairs with 21 chromosomes and 7,651 genes. This has

enabled a comparison of genome information for O. tauri

and O. lucimarinus. In a comparison to chromosomes 2 and

18 of O. lucimarinus, which correspond to chromosomes 2

and 19 of O. tauri, it was found that the chromosomes of O.

tauri exhibited marked differences in composition. More-

over, chromosome 21 of O. lucimarinus is comprised of

parts of chromosomes 9 and 13 of O. tauri. It was found that

chromosome 21 arose recently from duplication and fusion

of the chromosomes. It would be enlightening to cross these

two species and observe the meiosis process to examine the

changes in chromosome composition and investigate the

correlation with the speciation. However, sexual repro-

duction has not been recorded for these algae to date.

Chlamydomonas reinhardtii

Chlamydomonas is one of the most popular algae used in

experimental studies (Harris 2001). This alga has been used

for many years in studies of genetics, biochemistry and cell

biology as a model experimental organism. In addition to a

long history of classical biological experiments, research

into the molecular biology of Chlamydomonas has also

shown marked developments recently. The key advantages

of C. reinhardtii for studies of photosynthesis is their

ability to grow either photoautotrophically or heterotro-

phically (using acetate as the sole source of carbon) and to

assemble its photosynthetic apparatus in the dark. Dark-

J Plant Res (2008) 121:3–17 7

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grown cells, grown with acetate medium, maintain normal

chloroplast structure (Harris 1989; Dent et al. 2001). In

addition, the characteristic of the algae to move using two

flagellae has greatly contributed to flagellum movement

analysis of eukaryotes. Another advantage of this organism

is its susceptability to gene introduction methods, both to

the plastid (Boynton et al. 1988; Newman et al. 1990) and

the established nucleus (Debuchy et al. 1989; Kindle et al.

1989; Shimogawara et al. 1998). Because various markers

and introduction methods have been established, tagged

genes in the nuclear genome can be picked up and cloned

(Tam and Lefebvre 1993). The genomes of mitochondria

and chloroplast have been sequenced. The mitochondria

genome of C. reinhardtti is a linear molecule with a length

of 15.7 kb, and has only eight protein coding genes (Boer

et al. 1985). Most mitochondrial genomes of photosyn-

thetic organisms are circular molecules; so C. reinhardtti is

very unusual. On the other hand, the chloroplast genome

consists of circular molecules with an inverted repeat

similar to the general form for photosynthetic eukaryotes

(Maul et al. 2002). The construction of and phenotype

analyses for various genes have been examined using

genetic recombination techniques. Chlamydomonas is the

most suitable organism for analyzing molecular mecha-

nisms of replication, transcription and recombination of the

chloroplast genome. The atypical composition of the

nuclear genome was suggested prior to genome analysis. In

particular, the high ratio of GC content for the non-coding

region is an extremely unique characteristic. It was thought

that this high GC content (about 64%) of nuclear DNA

interfered with the sequencing analysis. Finally, the outline

of the draft genome sequence was recently completed. The

genome size is approximately 120 million base pairs with

17 chromosomes (Grossman et al. 2003; Table 2). The size

of this genome is almost the same as that of the nuclear

genome of the Arabidopsis thaliana, which is a model land

plant. However, 1,557 scaffolds still exist (version 3.0 data

from JGI: http://genome.jgi-psf.org/Chlre3/Chlre3.home.

html). Because contigs are not assigned on each chromo-

some, the sizes of the individual chromosomes cannot be

determined from the results of the genome analysis.

Recently, a karyotype with sufficient resolution has been

reported which disputes the number and genome size of the

chromosomes in C. reinhardtii (Aoyama et al. 2007). This

result should prove useful in the estimation of chromosome

size. It would be preferable to fill the remaining gaps

between contigs and assign them on the 17 chromosomes.

Fig. 3a–g Phase contrast/

fluorescent (a, b, f), fluorescent

(c, e, g) and phase-contrast (d)

photomicrograph images of O.tauri (a, c–g) and C. merolaecells (b–g) with chloroplasts

(red autofluorescence) after

staining with DAPI. The O.tauri cells (a, c–g) are smaller

than the C. merolae cells (b–g).

By contrast, the fluorescent

intensity of the O. tauri cell

nuclei (small arrowheads in cand e) is higher than that of the

nuclei in C. merolae (largearrowhead in e) (Kuroiwa et al.

2004). Scale bar 1 lm

Table 3 Fluorescent intensities (number of photons) of O. tauri and

C. merolae cell nuclei

O. tauri C. merolaeA B A/B

DAPI 1,134 9 103 455 9 103 2.5

SYBR Green I 21,983 9 103 6,398 9 103 3.4

A and B are the mean photon counts over the whole area every second

after staining with DAPI or SYBR Green I (Kuroiwa et al. 2004)

8 J Plant Res (2008) 121:3–17

123

These contigs contain over 15,000 predicted genes. The

known functional proportion of the genes is predicted to be

two-thirds, and the function of the remaining genes is still

unknown. These genes are annotated by members of the

Chlamydomonas Community.

Thalassiosira pseudonana

Diatoms are unicellular eukaryotic algae with unique pig-

ments and an ornate silica casing. These algae are found

throughout marine and freshwater ecosystems and may be

responsible for as much as 20% of global primary pro-

ductivity. Diatoms are the main primary producer in the

oceans. The most characteristic feature of diatoms is the

form of the silicified cell wall that consists of silicic acid

outside the cell (Table 1). The cell walls display species-

specific nanostructures of extremely fine detail. Genome

analysis of diatoms has been motivated by considerations

of their ecological and evolutionary importance. The dia-

tom on average contains a several-hundred mega base pair

genome (Veldhuis et al. 1997). T. pseudonana was con-

sidered to be suitable for complete genome analysis

because of its comparatively small genome size. The

genome of T. pseudonana was sequenced in 2004, pro-

viding a clear outline (Armbrust et al. 2004). Twenty-four

pairs of nuclear chromosomes ranging in size from 0.66 to

3.32 Mb were characterized based on sequence analyses,

giving a total of 34.5 million base pairs (Table 2). The

genome size from v3.0 assembled data from JGI was 31.3

million base pairs (http://genome.jgi-psf.org/Thaps3/

Thaps3.home.html). The genomes of the mitochondria

and chloroplast were also sequenced in 2005 and 2006,

respectively, and information on all three genomes is now

available.

Biological analyses based on genome information

Figure 4 summarizes the repertoire of proteins in each

organism based on their assignment to eukaryotic clusters

of orthologous groups (KOGs). The distribution of the

functional classification of each alga shows the ratio of the

gene compositions according to their characteristics. The

distributions were, on the whole, similar for C. merolae and

O. tauri, which have a similar genome size. The extremely

low proportion of genes for the cytoskeleton found in C.

merolae, as compared with the other organisms, might

reflect its simple cellular organization and systems. As

compared with the others, the rate of occurrence of genes

related to transcription, signal transduction mechanisms,

and extracellular structures is very high in C. reinhardtii.

This would reflect its comparatively complicated cell

structure and life cycle. The ratio of the genes related to

nuclear structure is markedly higher in T. pseudonana

compared to the other functional categories. Although many

genes related to the nuclear structure are assigned and are

nucleolar GTP/ATPase, the reason for this is unknown. The

C. mer

olae

O. tau

ri

C. rein

hard

tii

T. pse

udon

ana

Function unknown General function prediction only Secondary metabolites biosynthesis, transport and catabolism Inorganic ion transport and metabolism Lipid transport and metabolism Coenzyme transport and metabolism Nucleotide transport and metabolism Amino acid transport and metabolism Carbohydrate transport and metabolism Energy production and conversion Posttranslational modification, protein turnover, chaperones Intracellular trafficking, secretion, and vesicular transport Extracellular structures CytoskeletonCell motility Cell wall/membrane/envelope biogenesis Signal transduction mechanisms Defense mechanisms Nuclear structure Cell cycle control, cell division, chromosome partitioningChromatin structure and dynamics Replication, recombination and repair TranscriptionRNA processing and modificationTranslation, ribosomal structure and biogenesis

Fig. 4 Comparison of the

functional classifications of

proteins among four unicellular

algae. Columns represent the

proportion of proteins assigned

to the KOG classification of

each organism, C. merolae,

O. tauri, C. reinhardtti and

T. pseudonana, in a left to light

fashion. The actual numbers of

proteins assigned to each

classification in O. tauri,C. reinhardtti and T.pseudonana were obtained

from the JGI website

(http://www.jgi.doe.gov/)

J Plant Res (2008) 121:3–17 9

123

global image of gene composition among the four algae is

as has been shown above. Considering their unique meta-

bolic systems, some of the biological phenomena analyzed

using this genome information are described below.

Analyses related to cellular metabolism

Sulfate metabolism in C. merolae

Since C. merolae inhabits extreme (high-temperature,

strongly acidic) environments, it makes an interesting

subject for investigating metabolic systems adapted for

such extreme conditions. Its sulfur metabolism has been

particularly well investigated, since C. merolae lives in hot

springs typified by high sufide levels. Assimilation is the

only way to convert inorganic sulfur to organic sulfur.

Cysteine is the primary sulfur-containing compound and is

used along with other organic compounds. In photosyn-

thetic eukaryotes, two genes encode the key enzymes in

cysteine synthesis: O-acetylserine thiol liase (OASTL) and

serine acetyl transferase (SAT). OASTL catalyzes the

synthesis of cysteine from sulfide and O-acetylserine,

which is synthesized from serine and acetyl-CoA by SAT.

C. merolae is a good model organism for studies of

adaptation to this environment and the related metabolic

system. The two genes coding for OASTL and SAT were

isolated from C. merolae (i.e., four genes in total) (Toda

et al. 1998, 2001). SAT and OASTL have been demon-

strated to be active in three cellular compartments in higher

plants—cytoplasm, mitochondria and plastid. All four

genes of C. merolae were predicted to be of the organellar

types. Interestingly, OASTLs of C. merolae were derived

from both bacterial and eukaryotic origins, whilst SAT

genes belonged to the bacteria family. Transcription of all

of these genes has been confirmed using EST analysis,

suggesting that all of these genes are functional and that

sulfur metabolism systems of C. merolae utilize different

pathways in different compartments. Complementary

experiments using E. coli to investigate different properties

of OSATLs also suggest distinct sulfur metabolic pathways

in different subcellular components, most probably the

chloroplast and mitochondrion. It has also been suggested,

from the KEGG results, that many genes concerned with

the metabolism of cysteine were also encoded in the C.

merolae genome.

Lipid metabolism in C. merolae

The entire picture for the lipid metabolism system of C.

merolae has been described recently using biochemistry

and bioinformatics (Sato and Moriyama 2007). Acyl lipids

are very important to the formation of the plastid mem-

brane in photosynthetic organisms, and they are

synthesized using prokaryotic and eukaryotic pathways,

which exist in the plastid and the endoplasmic reticulum

respectively. All of the glycerolipids in photosynthetic

algae have been found in most studies. In the case of C.

merolae, the fatty acid composition was very simple, with

palmitic, stearic, oleic, and linoleic acids being the major

acids found. Unsaturated fatty acids containing two or

more double bonds were not detected experimentally and

major desaturase genes, such as acyl lipid desaturases of

cyanobacterial origin and stearoyl acyl carrier protein

desaturase, which is generally conserved in land plants and

green algae, were not detected in C. merolae from genome

information. These results suggest that polyunsaturated

fatty acids are not indispensable to photosynthetic organ-

isms. It has been clearly shown, for the first time, from the

genome information of C. merolae and experimental

results for lipid biosynthesis, that lipid synthetic pathways

differ in green and red algae.

Photosynthesis and selenoprotein genes in O. tauri

Ostrecoccus tauri displays some unique characteristics

with respect to photosynthesis. The alga lacks some genes

of importance to the light-harvesting complexes (LHC) of

photosystem II, but maintains other LHCI antenna protein

genes (Derelle et al. 2006). Furthermore, this unicellular

alga has all of the genes for C4 photosynthesis without the

mechanism for concentrating carbon dioxide. It is very

interesting that these genes exist even though the C4

photosynthesis system cannot actually function in this

organism. The existence of unique metabolic systems for

carbon dioxide fixation are expected from the variation of

the genes related to photosynthesis, but these need exper-

imental verification. The genes of a transport system for

nitrogen metabolism have also been completely identified.

However, whether the gene products, transporters, actually

function effectively in the uptake of the nitrogen source is

not known. While there seems to be a close relationship

between the amount of nitrogen supplied and the induction

of gametes for many algae, the sexual reproduction process

has not yet been recorded for this alga. As studies regarding

the relationship between nitrogen metabolism and gamete

genesis progress, particular characteristics may become

clear. Ostreococcus has genes for a large proportion of

selenocysteine-containing proteins relative to its genome

size (Palenik et al. 2007). O. tauri has 26 selenocysteine-

containing genes, while C. reinhardtii, with a genome size

ten times that of O. tauri, has only 12 genes including

selenocysteine (Lobanov et al. 2007). One major category

of the selenoproteins in Ostreococcus is the glutathione

10 J Plant Res (2008) 121:3–17

123

peroxidases. There is a possibility that these genes are

related to stress defense. The detailed function and mean-

ing of selenoproteins in eukaryotes remain unknown. O.

tauri, which holds many copies of selenoproteins, is a

material suited to studies of their function and it is hoped

that detailed cytological analyses of the proteins can be

performed. Genes commonly associated with the uptake of

metal ions do not exist in O. tauri; thus a special mecha-

nism, different from the general mechanism used by other

algae, seems to be used. In particular, mechanisms con-

cerning Fe uptake are peculiar to O. tauri. With respect to

the metabolism of trace elements, the genes for biosyn-

thesizing vitamin 12 do not exist at all. This alga seems to

depend on extraction of vitamin 12 from the external

environment and it uses substrates to synthesize

methionine.

Frustule biogenesis in T. pseudonana

The most distinctive aspect of diatoms is the frustule,

which consists of hydrated silicon dioxide (silica). The

silica structure is formed by expanding and molding the

membrane-bound silica deposition vesicle. Most of the

biosyntheses and biochemistry relating to the silicon frus-

tule are still to be elucidated. As a result of genome

analysis, three genes encoding transporters for active

uptake of silicic acid have been identified (Armbrust et al.

2004). The results from experiments on transcriptional

activities and the protein levels for these genes, performed

using a synchronized culture, indicated that a major regu-

latory step for SIT expression occurs at the translational or

post-translational level, and that SIT activity is controlled

largely by intracellular processes and not by protein levels

(Thamatrakoln and Hildebrand 2007). To study molecular

components of the silica deposition vesicle, and in partic-

ular membrane-associated proteins involved in structure

formation, isolated cell wall fraction proteomes from the

synchronized culture of T. pseudonana have been analyzed

(Frigeri et al. 2006). Tandem mass spectrometric analysis

based on sequenced genome information identified 31

proteins in the fraction. The patterns of the transcripts

according to the cell cycle have been analyzed with respect

to these protein-encoding genes, and a relationship to

frustule formation has been suggested. In particular, glu-

tamate acetyltransferase, which is one of the genes related

to the synthesis of polyamine, was identified in the fraction.

The expression patterns of mRNA for other genes in the

polyamine biosynthesis pathway were then analyzed during

cell wall synthesis. Three genes (ornithine decarboxylase,

ornithine carbamoyltransferase, and S-adenosylmethionine

decarboxylase) were correlated to the timing of cell wall

synthesis. To confirm that the genes of polyamine

biosynthesis identified in this way actually took part in the

synthesis of the cell wall, experiments were carried out

using an inhibitor. Cells treated with 10 mM 1,3-diami-

noproprane dihydrochloride, which inhibits polyamine

biosynthesis, were inhibited to about 10% of the growth of

untreated cells and had a rounded morphology. As valves

from the treated culture were incompletely formed, it was

suggested that some polyamines are crucial to valve for-

mation (Frigeri et al. 2006). A unique feature of diatoms is

their ornately patterned frustule that displays species-spe-

cific nanostructures. Recent attention has focused on the

biosynthesis of frustules and their nanostructures as a

paradigm for future silica nanotechnology. Studies in this

field will progress based on genomic information. By

combining transformation methods, it should become

possible to gain a much better understanding of the

molecular mechanism of frustule formation in the future.

Post-genome analyses in C. reinhardtii

Chlamydomonas reinhardtii is a good experimental model

to use to investigate the structure and organization of

photosystems, chloroplast biogenesis, the construction of

the flagellar apparatus, the sexual reproduction process, the

uniparental inheritance of the organelle genome, adaptation

to various environments, and circadian rhythms via various

molecular biology and genetic techniques. Proteomics or

transcriptomics, based on the available genomic resources,

has begun to reveal new details in each field of research. In

particular, analyses focusing on proteomes have already

provided new insights into the dynamics and compositions

of the photosynthetic apparatus, the chloroplast ribosome,

the respiration machinery of the mitochondria, phospho-

proteome, and the flagellum. DNA microarrays and

macroarrays have been used to study transcriptomes of

carbon-concentrating mechanisms (CCMs) in C. rein-

hardtii (Im et al. 2003; Miura et al. 2004; Yoshioka et al.

2004). Recent improvements to microarray techniques

have also been applied to the analysis of other metabolic

systems (Zhang et al. 2004; Eberhard et al. 2006). Prote-

ome analyses are generally used to understand the

construction of the photosynthetic apparatus (Yamaguchi

et al. 2003; Stauber et al. 2003; Turkina et al. 2006; Gillet

et al. 2006; Schmidt et al. 2006), light and circadian pro-

grams (Wagner et al 2004), the composition of

mitochondrial protein components (Lis et al. 2003), and so

on. A large number of different mutant loci have also been

shown to affect the assembly and function of the flagellar

apparatus. Biochemical analyses of wild-type and mutant-

type flagella have demonstrated that the flagellar axoneme

alone is composed of more than 200 proteins (Dutcher

1995). Proteomic analyses have been performed on the

J Plant Res (2008) 121:3–17 11

123

polypeptide components of the flagella and basal body (Li

et al., 2004; Keller et al. 2005; Pazour et al. 2005; Yang

et al. 2006). These post-genome analyses will be exten-

sively utilized, in combination with existing genetic,

biochemical, and molecular tools, in future algal studies

(Stauber and Hippler 2004).

Genome information for C. reinhardtii will be useful for

studies into the proliferation or inheritance of chloroplasts.

Chloroplasts multiply after the replication and distribution

of chloroplast DNA; however, the detailed mechanisms of

DNA transmission are not well understood. The moc

mutants of the altered localization and distribution of

chloroplast DNA have been isolated (Misumi et al. 1999);

thus, the molecular mechanisms of the transmission of

genetic information during vegetative proliferation should

be elucidated based on the genome information. On the

other hand, the uniparental inheritance of chloroplast and

mitochondrial genomes during the sexual reproduction

process is a universal trait among the eukaryotes, from

algae to vertebrates (Kuroiwa 1991; Gillham 1994; Ni-

shimura et al. 2002, 2006). The processes of the

degradation of organelle DNA during sexual reproduction

have been well studied using C. reinhardtii as a model

system (Kuroiwa et al. 1982, 1985; Kuroiwa 1991; Aoy-

ama et al. 2006). It is now thought that uniparental

inheritance is achieved through active processes, including

the rapid digestion, protection, and amplification of orga-

nelle DNA. Though the disappearance of organelle DNA in

accord with the course of the sexual reproduction process

from gametogenesis to meiosis has been examined cyto-

logically, the detailed molecular mechanism and the genes

related to it are not well understood. Genes encoding these

factors should be found in the future by mass spectrometry

analysis based on the genome information presently ana-

lyzed (Ogawa and Kuroiwa 1986, 1987, 1985; Uchida et al.

1992, 1993; Nishimura et al. 1999, 2002). Our research

target is to clarify the mechanisms of uniparental inheri-

tance shown in Fig. 5 based on the genome information for

C. reinhardtii.

Studies of organelle proliferation based on genome

information for C. merolae

The use of sequenced genome information to elucidate the

biological phenomena is important. One example is a study

relating to the mechanism of organelle division in C.

merolae. Initially, synchronization of cell cycles with light/

dark cycles was established in C. merolae (Suzuki et al.

1994; Terui et al. 1995) and the division process of the cell

was analyzed in detail cytologically prior to studies of

organelle division (Miyagishima et al. 1999a; Misumi et al.

2005). Neither phytochrome nor phototropin, both of which

are so-called photoreceptors, exist in C. merolae even

though the synchronization of the cell cycle is induced

using light (Matsuzaki et al. 2004). The existence of an

unknown light receptor mechanism is suggested. More-

over, importantly, the condition of isolation of each

organelle has been examined in detail (Miyagishima et al.

1999b, 2001a; Yoshida et al. 2006; Nishida et al. 2007;

Yagisawa et al. 2007). The basic processes of mitosis that

have been analyzed in C. merolae cell so far are repre-

sented in Fig. 6. During interphase, the centrosome forms

the focus for the interphase microtubule array outside the

nucleus. By early prophase, the centrosome and the Golgi

apparatus divide, and the resulting two asters and the Golgi

apparatus move apart. Chromosomal condensation does not

Fig. 5 Model for the molecular mechanism of uniparental inheri-

tance in C. reinhardtii based on the active digestion of mt- cpDNA

by Mt+-specific DNase (MDN). In vegetative cells, MDN is absent or

inactivated in both mating types. During gametogenesis, MDN is

synthesized or activated only in mt+ cells. At the same time, mt+

cpDNA becomes resistant to the action of MDN. During gamete

fusion, MDN obtains access to unprotected mt- chloroplasts and

digests mt- cpDNA, leading to the uniparental inheritance of

cpDNA. Several factors may mediate the successful digestion of

mt- cpDNA after zygote formation: (1) entry of MDN into mt-

chloroplasts; (2) efficient access of MDN to cpDNA molecules; and

(3) an increase in Ca2+ inside mt- chloroplasts. Zygote-specific gene

expression may be crucial to these processes (Nishimura et al. 2002)

12 J Plant Res (2008) 121:3–17

123

occur during prophase. Plastid and mitochondrial divisions

start in this order in late G2 and end by the metaphase. The

dynamic trio of rings control mitochondrial and plastid

divisions. Microbody and lysosomes associate with the

dividing V-shaped mitochondrion. At metaphase and early

anaphase, the bipolar structure of the spindle is clear, and

all chromosomes appear to be aligned at the equator of the

spindle. However, individual chromosomes cannot be

identified. Plastid and mitochondrial divisions finish by

metaphase, at which time division of the microbody starts.

The connecting bridge between daughter mitochondrion

and the microbody appears to play an important role in

microbody division. At anaphase, sister chromatids sepa-

rate synchronously, and daughter chromosomes begin to

move toward the poles. Although this alga has the full

complement of genes concerned with chromosome con-

densation (Hirano 2005), chromosomal condensation never

occurs during mitosis in C. merolae. At telophase, the

daughter nuclei and nucleoli reform, and division of the

microbody may occur through the connecting bridge. By

late telophase, cytokinesis is almost complete. Although

the typical actin gene is encoded in the genome, tran-

scription of the gene does not occur and the gene product

was not detected (Takahashi et al. 1998). In addition, no

genes encoding myosin were found. C. merolae cells

therefore seem to divide using a system other than that of

actomyosin. The mitochondrion, lysosome and microbody

behave as if they are linked. At the final stage of cell

division, a tiny contractile-like ring appears at the equator

of the cell.

The electron-dense plastid dividing ring (PD ring) was

first identified outside the plastid envelope at the con-

stricted site of the dividing chloroplast in C. caldarium,

which is a close relation of C. merolae (Mita et al. 1986;

Mita and Kuroiwa 1988). Presently, the favored organism

for studies of organelle division has changed to C. merolae

due to its large division ring and simpler structure. In 1993,

electron-dense deposits in the equatorial region of the

dividing mitochondria were first identified after an exten-

sive search for a mitochondrial dividing ring (MD ring)

throughout the cell and life cycles of C. merolae (Kuroiwa

et al. 1993). Research at the molecular level concerning the

organelle division has advanced notably through the use of

of synchronized culture techniques and isolation systems

using C. merolae with its obvious division apparatus

(Miyagishima et al 2001a, b; Nishida et al. 2005). Recent

studies have shown strong similarities between plastid and

mitochondrial division (Takahara et al. 2000; Miyagishima

et al. 2003; Nishida et al. 2003; Kuroiwa et al. 2006;

Miyagishima and Kuroiwa 2006).

The division of plastids and mitochondria mainly

involves a dynamic trio: an FtsZ ring of bacterial origin,

electron-dense PD/MD rings, and eukaryotic dynamin

rings (Miyagishima et al. 2001b, 2003; Nishida et al. 2003;

Kuroiwa et al. 2006; Miyagishima and Kuroiwa 2006).

Four genes represent mitochondrial FtsZ (FtsZ2-1 and

f g h i j

LYMI

NCEN

G

M

P

ER

NMP

NLO

a b c d e

Fig. 6a–j The basic course of mitosis in a C. merolae cell.

Illustrations show the behavior of cellular components during mitosis.

Phase contrast–fluorescent images of C. merolae interphase (a) and

dividing cells (b–e) showing the localization of nuclear (N),

mitochondrial (M), and plastid DNA (P in blue/white) after DAPI

staining are shown. The plastids emit red autofluorescence. Divisions

of the plastid, mitochondrion, and nucleus occur in this order (a–e).

During late G2 (a) and prophase (b), the plastid and mitochondrial

divisions advance and finish by the metaphase (c). At anaphase, the

chromatids begin to move toward the poles, but each chromatid

cannot be identified (d). Chromosomes do not condense during

mitosis. Cytokinesis starts from the plastid side and closes between

daughter nuclei (e). Scale bar in e 1 lm. Schematic representation of

C. merolae interphase (f) and dividing cells (g–j); cell contains basic

organelles [a nucleus (N), a mitochondrion (M), and a plastid (P), ER,

a Golgi apparatus (G), lysosomes (LY), and a microbody (MI)]. The

nucleus has a nucleolus (NLO), and the mitochondrion and plastids

contain their own nuclei (nucleoids) in the center (blue), respectively

(Misumi et al. 2005)

J Plant Res (2008) 121:3–17 13

123

FtsZ2-2) and plastid FtsZ (FtsZ1-1 and FtsZ1-2), both of

which form early at the site of future division, before the

formation of PD/MD rings can be confirmed by genome

analysis (Matsuzaki et al. 2004). Only two dynamin genes

(Dnm1 and Dnm2) have been found, that play roles in the

later stages of mitochondrion and plastid membrane fission,

respectively. These findings suggest that both mitochondria

and plastids in early eukaryotes exhibit similar division

apparatus consisting of complexes of bacterial and

eukaryotic rings. Components other than this main

dynamic trio are being identified using highly synchronized

cultures and fractionation of division machinery of C.

merolae. When the nucleotide sequence of an entire gen-

ome is sequenced, target genes can be identified from

peptide mass fingerprints of ultrasmall quantities of pro-

teins. Recently, part of the mitochondrial division

machinery was purified from M phase-arrested C. merolae

cells through biochemical fractionation. The dynamin-

related protein Dnm1 was one of the two major proteins in

the purified fraction and was accompanied by a protein,

Mda1, newly identified by the matrix-assisted laser

desorption/ionization time-of-flight mass spectrometry

(MALDI-TOFMS) method. Mda1 forms a stable homo-

oligomer by itself and the protein participates in the

mitochondrial division machinery as a core component

(Nishida et al. 2007). Studies on chloroplast division have

made similar progress. Isolates of (plastid-dividing, dyn-

amin, and FtsZ) PDF machineries from dividing

chloroplasts were obtained from synchronized cells and

treated with detergents. The proteome of the isolated PDF

machineries was examined using SDS-polyacrylamide gel

electrophoresis, MALDI-TOF-MS and immunoblotting

analysis. A number of novel proteins as well as those

already known, such as dynamin, were identified in the

proteome of the isolated PDF machineries (Yoshida et al.

2006). It was suggested that these components were the

motive power for sliding bundles. As a result, the detailed

molecular mechanisms of chloroplast division by PDF

machineries were proposed (Fig. 7). The functions of

several components of these machineries are currently

being elucidated. In addition, experiments to discover

novel genes related to the multiplication of organelles from

transcriptome analysis have been performed using highly

synchronized cultures and oligonucleotide microarrays

Fig. 7 Model of chloroplast

division by PDF machinery. In

the first step, the GTPase

dynamin molecules in the PDF

machinery probably function as

cross-bridges or covers that

undergo microscopic

movements to drive the sliding

of the 5–7 nm filaments in the

PD ring during the early phase

of chloroplast division. The

dynamin ring generates the

dividing force for contraction

with the aid of the other rings.

In the second step, the dynamin

molecules move from the

surface of the PDF machinery to

the inside of the machinery and

play a role in pinching off the

narrow bridge between daughter

chloroplasts during the late

phase of chloroplast division

(Yoshida et al. 2006)

14 J Plant Res (2008) 121:3–17

123

containing all of the nuclear, mitochondrion and chloro-

plast genes (T. Fujiwara et al., unpublished results). Many

genetic candidates related to the proliferation of the cell

and organelles have been identified from this experiment.

Thus, research into cell or organelle proliferation using C.

merolae has advanced notably using a combination of the

genome information and established experimental

techniques.

Conclusion

The algal genome sequences revealed that individual

organisms possess unique features in terms of primary

sequence structures and gene compositions, making each

useful for understanding basic physiological aspects and

the evolution of photosynthetic eukaryotes. When investi-

gating the maintenance of common cellular components,

each algal genome project provides enough genome

sequence data to allow comparative orthologous analysis of

each algal genome. Since such research is based on small

genome repertoires, particularly for unicellular algae, algal

genome information should accelerate studies on, for

example, the establishment of cellular components, and it

will allow us to elucidate cellular and molecular properties

that are they have in common with land plants or other

eukaryotes.

Genome projects are being generated for the green alga

Chlorella vulgaris, Dunaliella salina, Micromonas pusilla,

and Volvox carteri, the red alga Galdieria sulphuraria, and

the haptophyte Emiliania huxleyi, among others. Genome

sequence analyses of other algae are also now in progress.

It is very important to study a variety of species, repre-

senting algae from different phylogenetic groups, which

exhibit both unique and important biological

characteristics.

Genetic manipulation methods have been developed and

reported for various algae. C. reinhardtii is known to be the

best model organism for studies of molecular biology with

transformation techniques for both plastids and nucleus.

Recent developments allow gene function to be evaluated

using RNAi suppression of gene activity, and GFP fusion

proteins are available to elucidate localization of gene

products. On the other hand, transformation experiments

are also reported, such as those for C. merolae (Minoda

et al. 2004) and several diatoms (Dunahey et al. 1995; Apt

et al. 1996, 2002; Falciatore et al. 1999). If functional

analysis using gene disruption becomes possible by

improving gene manipulation methods for these species,

algae will become very useful in many research fields. A

number of notable advances in our understanding of mor-

phological, physiological and evolutionary aspects have

been made so far. Needless to say, future proteomic and

gene-targeting analyses promise to accelerate our under-

standing of these vital features of photosynthetic

eukaryotes, including land plants. In particular, studies

based on the three genome sequences (nuclear, mitochon-

drion and plastid), which all provide substantial genetic

information on eukaryotes, are possible with C. merolae.

In addition, as revealed by its recently completed

genome sequence (Nozaki et al. 2007), the smallest

known histone-gene cluster, a very low density of

the number of chromosomes which encode the histone genes

ANDr fo rebmun eht

stes

nortni htiw seneg

deipucco oitar eht

osopsnart yb

snemoneg a ni

sene

g de

docn

e ni

etor

p fo r

ebmu

n eh

t

1

3

0.5%

0.7%

4,775

Cyanidioschyzon merolae

4-200

O. tauri, C. reinhardtii, T. pseudonana

7<

2-10%

39 < % 7,892-15,000

Fig. 8 Nuclear genome

comparison of the four algal

species in a modified figure

(Nozaki et al. 2007;

http://www.biol.s.u-tokyo.ac.jp/

users/tayousei/labdetail.html).

The number of introns, the

number of rDNA sets, the

number of chromosomes which

encode the histone genes, the

proportion of the genome occu-

pied by transposons, and the

number of protein-encoded

genes are shown in the diagram.

The genome size and its orga-

nization significantly vary

between all four kinds of uni-

cellular algae. C. merolaeappears to have the simplest

nuclear genome and is extre-

mely useful for further studies

of eukaryotic cells

J Plant Res (2008) 121:3–17 15

123

transposable elements, and other previously described

simple features of the C. merolae nuclear genome are

very distinctive and constitute the simplest set of genomic

features found in any nonsymbiotic eukaryote yet studied

(Fig. 8). Therefore, C. merolae represents an ideal model

organism for studying the fundamental relationships

between information encoded on the three genomes

and the functions of organelles. Furthermore, because

C. merolae inhabits high-temperature environments (45–

50 �C), most of its proteins must be unusually heat-stable,

and so its proteome may well provide important new

insights into the structural analysis of proteins and their

heat stability.

Acknowledgments This work was supported by Grant-in-Aid for

Scientific Research A (No. 19207004 to TK), and by grants from

Frontier Project ‘‘Adaptation and Evolution of Extremophile’’ (to TK)

from the Ministry of Education, Culture, Sports, Science and Tech-

nology of Japan, and from the Program for the Promotion of Basic

Research Activities for Innovative Biosciences (PROBRAIN to TK).

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