A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes

Nelly Mostajo Berrospi; Marie Lataretu; Sebastian Krautwurst; Florian Mock; Daniel Desirò; Kevin Lamkiewicz; Maximilian Collatz; Andreas Schoen; Friedemann Weber; Manja Marz; Martin Hölzer

To validate the accuracy of our approach, we compared our miRDeep2 annotations of M. lucifugus/P. alecto (based on the transcriptomic data derived from M. daubentonii; Weber-2019) with annotations of miRNAs for transcriptomic data of Myotis myotis 8 and P. alecto 55 . For reference mapping, Huang et al. also used the M. lucifugus genome, so we were theoretically able to directly compare our annotations with the annotations of both studies. Unfortunately, no positional information (annotation file) of the identified miRNAs derived from the transcriptomic data of M. myotis were given in the manuscript or supplement 8 . Therefore, we blasted the precursor miRNA sequences identified with the help of the M. myotis transcriptome against the M. lucifugus genome and retained only hits with a sequence identity of 100 %. The so obtained positional information was further used to calculate the overlap between our predicted miRNAs in M. lucifugus. We used the same approach for the P. alecto comparison. If the annotated location of an miRNA and one of our identified miRNA locations in M. lucifugus/P.alecto were overlapping by at least 85 %, we counted this location as a common prediction.