624
Chlamydomonas
2.1
Nuclear Genome
The complexity of the nuclear genome of
C. reinhardtii
has been estimated at 1
×
10
5
kb. At least 17 nuclear linkage groups
have been identiFed with numerous mark-
ers
my
genome/nuclear
maps.html).
These
include
auxotrophic
mutations,
drug-
resistant
markers,
mutations
affecting
photosynthesis directly or indirectly, fla-
gellar function, and mating. The use of re-
striction fragment length polymorphisms
(R±LPs) to follow the segregation of
speciFc DNA fragments in the genome
has greatly accelerated genetic mapping.
Efforts to establish R±LP maps for sev-
eral of the nuclear linkage groups of
C.
reinhardtii
are under way. A large collec-
tion of BAC clones covering the nuclear
genome has been established and was used
to sequence the entire genome. Telomere
sequences from
C. reinhardtii
have been
isolated and characterized. They are found
at the chromosome ends with an average
length of 300 to 350 bp, and they consist of
the simple invariant repeat TTTTAGGG,
which is very similar to its counterpart in
Arabidopsis thaliana
. Telomere-associated
sequences, deFned as the sequences close
to the telomere repeats, appear to be useful
markers for establishing R±LP maps.
Many nuclear genes of
C. reinhardtii
have been characterized. Genes that are
highly expressed (e.g. those encoding pro-
teins of the photosynthetic and flagellar
apparatus or the heat shock proteins)
display a strong codon bias. In general,
cytidine (C) or guanine (G) residues at
the third position of the codons are most
common and, if possible, also in the Frst
position, reflecting the high GC content
(63%) of the nuclear DNA. However, genes
that are less expressed, such as cytochrome
c
6
and arylsulfatase, show a considerably
more balanced codon usage. An A-rich
sequence resembling the TATA box can
usually be recognized in the upstream re-
gion of the nuclear genes of
C. reinhardtii
with an adjacent GC-rich stretch. In all the
cases examined, a putative polyadenyla-
tion recognition motif TGTAA is found at
the 3
0
end, 10 to 15 nucleotides upstream
of the polyadenylation site. Another dis-
tinctive feature of the nuclear genes of
C.
reinhardtii
is the presence of multiple in-
trons. As an example, the gene of one heat
shock protein, hsp70, contains six introns,
whereas its counterpart in plants contains
only one intron, or none at all.
2.2
Chloroplast Genetic System
The chloroplast genome of
C. reinhardtii
has recently been sequenced and found
to consist of 204 kb circular molecules.
It is, therefore, larger than the plastid
genomes of land plants, which range
between 120 and 160 kb. Although the
informational content of this DNA is low,
about 0.2% of the cell DNA complexity,
it constitutes 10 to 15% of the cellular
DNA mass because it is present in
approximately 80 copies per cell, which
are arranged into 8 to 10 nucleoids within
each chloroplast. The chloroplast DNA of
C. reinhardtii
is AT-rich and, therefore, its
density differs considerably from that of
nuclear DNA. This property can be used for
purifying chloroplast DNA from total cell
DNA by density gradient centrifugation.
The striking differences in codon usage
between nuclear genes and chloroplast
genes suggest that these genomes are
distinct in origin, in agreement with
the endosymbiotic theory, according to
which chloroplasts have evolved from
photosynthetic prokaryotes that took up
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