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The copyright holder for this preprint (which was not peer-reviewed) is the .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 Table 5 : General genome information for each of the 16 investigated bat assemblies and selected ncRNA examples annotated in this study. We selected ncRNAs with interesting copy number distributions among the investigated bat species. For SNORA38, PVT1_5 and HOTTIP_2 and 3 we additionally found sophisticated differential expression patterns in at least one of the used RNA-Seq data sets (absolute log2 fold-change greater 1, TPM> 10). For all bat species we observed various numbers of tRNAs (Tab. 5 and Tab. S4). We could detect full sets of tRNAs for E. fuscus and M. davidii, whereas between one and four tRNAs are missing from the assemblies of H. armiger, M. brandtii, M. lucifugus, M. lyra, M. natalensis, P. parnellii, R. ferrumequinum, R. sinicus, and D. rotundus and between nine and twelve are missing for E. helvum, P. alecto, P. vampyrus, R. aegyptiacus, and E. spelaea (Tab. S4). Interestingly, we identified a large number of tRNAs (18, 235) for M. lyra in comparison to all other bat species (Tab. S4), likely a result of the low assembly quality (Fig. 2, Tab. S1 ). The lowest amount of tRNAs was annotated for P. parnellii and D. rotundus with only 1,059 and 1,041 copies, respectively. In all other bat genomes we found between 1,735 and 4,657 tRNA genes (Tab. S4). The tRNA encoding for valine (Val) with the anticodon structure TAC had high copy numbers (over 1,000) in all genome assemblies of the Pteropodidae family (Tab. 5). Similar copy numbers were achieved by the R. ferrumequinum and R. sinicus assemblies regarding the tRNA encoding for isoleucine (Ile) with the anticodon AAT (Tab. S4). For tRNA(Ile) and the anticodon GAT we also observed high copy numbers in H. armiger. Interestingly, all species with high tRNA(Val) and tRNA(Ile) copy numbers had rather low counts (between 0 and 28) of tRNA(SeC) with the anticodon TCA, while this tRNA was found with higher copy numbers in P. parnelli (68) and in D. rotundus (145) and with even higher counts (between 315-498) in all other bat species (Tab. S4). However, high copy numbers might be also occur due to assembly quality and false positive predictions of tRNAscan-SE.