Fig. 5

Alignment of RNA-Seq reads with poly(A) ends to mitochondrial genes. The last three codons and the stop codon are shown for each protein-coding gene (PGS) encoded on the heavy strand except for the upstream genes from both bicistronic transcripts (nad4l and atp8). An example poly(A) end-read (cDNA sequence) is shown aligned to the genomic (mtDNA) sequence. The sequence of the gene located immediately downstream of each PGC is shown over a length corresponding to the unaligned poly(A) end of the read. Only the first and last six nucleotides are shown in antisense sequences of the genes contained within the 3′ untranslated regions of cox1 (trnS) and nad5 (trnE and nad6), with their middle sections represented by ‘XXX’