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

As we annotated all bat assemblies by using different tools, we needed to merge the resulting GTF files to resolve overlapping annotations and to recieve a final annotation of ncRNAs for each bat species. Furthermore, we extended the available NCBI annotations (including proteinand non-coding genes) by integrating our novel ncRNA annotations. The scripts used to merge the different annotation files and to calculate overlaps between annotations can be found at https://github.com/rnajena/bats_ncrna. Due to their size, we have not included the lncRNA Table 3 : Mitochondrial bat genomes (mtDNA) publicly available and used for annotation with MITOS 57 . For 10 out of the 16 bat species investigated in this study, mtDNA could be found in the NCBI. For four bat species, the mtDNA is also part of the genome assembly as determined using BLASTn. For E. helvum, no mtDNA could be found in the NCBI, but we were able to identify a single contig that is part of the genome assembly as mtDNA using BLASTn and the mitochondrial genomes of the other bats as query. The contig was rearranged to match the gene order of the other mtDNAs. R -found via BLASTn and rearranged.