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

In this study, we comprehensively annotated ncRNAs in 16 readily available bat genomes obtained from the NCBI database (Tab. 1). We provide novel annotations in the common GTF format, following a hierarchical structure of gene, transcript, and exon features to allow direct integration of our annotations into already available ones (Tab. S3-S10). Finally, we provide for each bat genome assembly an extended annotation file merged with the protein-and non-coding gene annotations that were already available by the NCBI database (Files S1; leaving out potential lncRNAs that can be downloaded separately, see Tab. S9). We used six RNA-Seq data sets derived from the transcriptomic sequencing of four bat species (Tab. 2) to calculate normalized expression values for our newly annotated ncRNAs and exemplarily show significantly differential expressed ncRNAs (Fig. 4) , that were never before described on such a large scale for any bat species. In addition to the evolutionarily explainable differences in the pure existence and the amount of annotated ncRNAs in bats, we have observed that the assembly quality can also influence the annotation results. While the effects on the annotation of short ncRNAs seem to be small (with some exceptions), the number of identified author/funder. All rights reserved. No reuse allowed without permission.