2. 2. Determination of mitochondrial transcription pattern
PolyA (polyT in reverse direction) selection was applied to determine the polyadenylation patterns and relative abundances of mitochondrial monocistronic units. Firstly, reads from the RNA-seq data were reduced to only those containing polyA sequences with a minimum five bases in size at any end, using the manually written script in PERL (Appendix 1). Then, selected sequences with polyadenylation were aligned to the reference mitogenome with “map to reference” option and using the bowtie2 algorithm in Geneious R9.1.5 (https://www.geneious.com) (Kearse et al. , 2012) and their patterns were checked manually. Whole RNA-seq data without polyadenylation selection was also aligned to mitogenome, and RPKM (Reads Per Kilobase of transcript per Million mapped reads) values were calculated for each gene.