Gene map of Scenedesmus cpDNA and compared patterns of gene partitioning in Chlamydomonas and Scenedesmus cpDNAs. The two copies of the rRNA operon-containing IR (IRA and IRB) are represented by thick lines; the transcription direction of the rRNA genes is indicated by arrows. Genes (filled boxes) on the outside of the map are transcribed in a clockwise direction; those on the inside of the map are transcribed counterclockwise. The colour-code denotes the genomic regions containing the homologous genes in Chlamydomonas cpDNA: cyan, SC1; magenta, SC2; yellow, IR. Genes and ORFs absent from Chlamydomonas cpDNA are shown in grey. Labelled brackets denote the gene clusters shared specifically by Scenedesmus and Chlamydomonas cpDNAs (see Table 4 for the gene content of these clusters). tRNA genes are indicated by the one-letter amino acid code followed by the anticodon in parentheses (Me, elongator methionine: Mf, initiator methionine). Identical copies of the trnE(uuc) genes are denoted by asterisks. Introns are represented by open boxes and intron ORFs are denoted by narrow, filled boxes. The intron sequences bordering the psaA exons (psaA exon 1 and psaA exon 2) are spliced in trans at the RNA level. Note that only one of the two isomeric forms of the genome is shown here; these isomers differ with respect to the relative orientation of the single-copy regions.