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 genome assembly status of different bat species varies widely: ranging for example from 29,801 contigs and an N50 of 26,869,735 nt (D. rotundus) to 192,872 contigs and an N50 of only 16,881 nt (M. lyra), see Tab. 1 and Tab. S1. Accordingly, also the annotation status varies a lot (Tab. 4). Within this work, we give an overview of potential ncRNA annotations in bats. However, the precise number of ncRNAs remains unclear, because of ncRNAs being present several times in the assemblies, and others still remaining undiscovered. To give a better estimation of transcribed and potentially functional ncRNAs, we used six Illumina short-read RNA-Seq data sets derived from four bat species (Tab. 2) to estimate the expression levels of our novel annotations. Note that we refer throughout this paper to an RNA-Seq data set by the first author's name and the year of the respective data set publication. The only included data set derived from a species of the Yinpterochiroptera suborder (R. aegyptiacus) was obtained from a study dealing with the differential transcriptional responses of Ebola and Marburg virus infections in human and bat cells 16 (data set: Hölzer-2016). In this study, total RNA of nine samples of R06E-J cells, either challenged by the Ebola or Marburg virus or left un-infected, were harvested at 3, 7, or 23 h post infection (poi) and sequenced. Unfortunately, no biological replicates could be generated for this study. Therefore, we did not use this data set for the differential expression analysis, but also Finally, we used data of the long-fingered bat M. natalensis initially obtained to characterize the developing bat wing 33 . Here, total RNA was extracted from paired forelimbs and hindlimbs from three individuals at three developmental stage.