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

At best, a genome assembly represents the full genetic content of a species at chromosome level. Whereas the first complex eukaryotic genomes were generated using Sanger chemistry, todays technologies such as Illumina short-read sequencing and PacBio or Oxford Nanopore long-read approaches are increasingly used 58 . The currently available bat genomes vary wiedly regarding their assembly quality and completness (Tab. 1, Fig. 2 , and Tab. S1) and were predominantly assembled by using short Illumina-derived reads and low (∼18 X) 28 up to moderate/higher coverage (77-218 X) approaches 25, 26, [30] [31] [32] [33] . A new assembly of the cave nectar bat (Eonycteris spelaea) 29 was exclusivly generated from longread data derived from the PacBio platform and the genome of the Egyptian fruit bat (Rousettus aegyptiacus) 27 was assembled by using a hybrid-approach of Illumina and PacBio data. These two genomes from the Pteropodidae family are of a generally higher quality (Fig. 2 , Tab. S1). Regardless of their assembly quality, these genomes need to be annotated to identify regions of interest, for example, encoding for protein-and non-coding genes or other regulatory elements.