Sequencing and analysis of the chloroplast genome of
Cyanidium caldarium RK1

The organism C. caldarium RK1 is a unicellular red alga.

We propose it as a simple model red algal cell. The features of its chloroplast genome seem to resemble a very old stage in plastid development.

For more details read the abstract of the paper published in J. Mol. Evol. (2000) Oct;51(4):382-90

 Table 1: The Cyanidium caldarium RK1 chloroplast genome in numbers

size 164921 bp
% GC 32.7
size of direct repeat 186 bp
noncoding 17399 bp
coding 147522 bp
genes 232
             orfs 199
             RNAs 33
av. intergenic spacer size 71 bp

Gene classes on the C. caldarium plastome

 Table 2:  Classification of the chloroplast genes

Amino acid biosynthesis 8
Biosynthesis of cofactors, prosthetic groups, and carriers 12
Cell envelope 2
Cellular processes 6
Central intermediary metabolism 1
Energy metabolism 2
Fatty acid, phospholipid, and sterol metabolism 5
Photosynthesis and respiration 54
Regulatory functions 3
DNA replication, restriction, modification, recombination, and repair 1
Transcription 4
Translation 50
Translport and binding proteins 2
Hyhpothetical proteins 55
tRNAs 30
rRNAs 3
The genes found can be classified as shown in table 2. An additional table containing the protein locations, their sequences, their classification, and links to homologues genes can be found here. A linear map of the cp-genome includes the gene classifications.

Comparison with P. purpurea

Since the chloroplast genome sequence of a higher red alga Porphyra purpurea is known we compared the two genomes.
 Fig. 1 Synteny regions as detected via a simplot. The simplot tool (J. April, pers. com.) uses similarity scores to compare two sequences. The blue boxes represent the unique genes in each organism. The grey diagonal area marks the region in which local rearrangments occurred. One region cannot readily be aligned (grey rectangle).

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