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.