1. Analysis of the atp9 5‘ trailer A B At5S-5 Atatp9.Endo.Mega.A atp9 At5S-Mega.R (-239) (-84/- 83) (+180) 5S rRNA 5’ 3’ atp9 mRNA atp9 pre-mRNA atp9 5’ leader At5S-1 Atatp9-11 promoter primers used forprimer namelocation of the primer relative to the 5‘-terminal nucleotide of 5S rRNA (+1)*/atp9 start codon (+1)** and in nc_001284 synthesis of cDNA first strandAt5S-5+118* to +100* (361,062 to 361,080) PCR amplification 1Atatp9-Endo.Mega.A-239** to -208** (278,656 to 278,687) PCR amplification 1At5S-Mega.R+107* to +82* (361,073 to 361,098) PCR amplification 2Atatp9-11-203** to -186** (278,692 to 278,709) PCR amplification 2At5S-1+85* to +67* (361,095 to 361,113) atp9 5’ leader

2. 1. PCR I 2,000 bp 1,500 bp 750 bp 1,000 bp 250 bp 500 bp marker II 2,000 bp 1,500 bp 750 bp 1,000 bp 250//242 bp 500//501/489 bp 404 bp 331 bp 190 bp 147 bp 111/110 bp 2. PCR;on template I marker 1 2. PCR;on template II marker 2 III CD E transcript ends identified in the PCR products PCR product size of PCR product 5‘ end of 5S rRNA relative database entry (+1) 3‘ end of atp9 -leader relative to the start codon (+1) remarks I786/785/784 bp-2/-1/+1+438mature atp9 transcript II265/264/263 bp-2/-1/+1-84 III229/228/227 bp-2/-1/+1-84used for cloning

3. ends found in individual cDNA clones from pcr product III clone3‘ end position in the mitochondrial genome (nc_001284) 3‘ end position in respect to the ATG codon (-1) Non-encoded nucleotides #20278,710-185** #37278,749-146 #100278,766-129 #54278,777-118AAA #96278,777-118CGTCT #12278,778-117** #79278,784-111 #92278,784-111** #29278,797-98AA #41278,808-87* #33278,808-87* #65278,808-87* #73278,808-87 #84278,809-86* #48278,811-84 #59278,811-84 #97278,811-84AAAAAAAACAA */** A single* or two** nucleotide(s) at the ligation site could be either assigned to atp9 or 5S rRNA. Thus the atp9 5’-leader ends either at the indicated position or one or two nucleotide(s) further downstream. F

4. Supplementary Figure 28. Analysis of the atp9 5‘ trailer. A modified CR-RT-PCR using endogenous 5S rRNA as adapter molecule was carried out to determine the 3’ end of the atp9 5’ trailer upstream of the mature atp9 transcript as outlined in (A). The site of the endonucleolytic cleavage is marked by a pair of scissors. The primers used are listed in table (B). The products of the first PCR amplification (marked by arrows and detailed in table (E)) were separated by agarose gel electrophoresis (C), excised and used as template for a second PCR amplification. PCR product I was additionally analyzed by direct sequencing. The products of the second PCR were again separated by agarose gel electrophoresis (D). PCR product III was cloned and individual clones were sequenced. The ends found in these clones are listed in table (F).