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

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/738526 doi: bioRxiv preprint GTF gene attribute field (Tab. S9). The scripts used for the identification of lncRNAs can be found at https://github.com/rnajena/bats_ncrna. For EHE we found a possible mtDNA contig in full-length (16,141 nt; AWHC01200796) in the genome assembly. Due to the circularization of mtDNA, we rearranged the sequence of this contig to start with the gene coding for the phenylalanin tRNA and to match the gene order of the other mitochondrial genomes. Only for ESP, RSI, MLY, EFU, and MNA, we were not able to detect any possible contigs of mtDNA (Tab. 3). All eleven mitochondrial genomes were annotated with MITOS 57 . The ncRNA results were filtered by e-value (threshold 0.001), thus one of two small rRNAs in MBR and RFE and one of two large rRNAs in EHE were discarded as false positive hits (Tab. S10). For the five bat assemblies directly including mtDNAs (Tab. 3), the MITOS annotations were added to the final merged ncRNA annotation. All other mtDNAs and annotations can be found in Tab. S10.