Preface

This online supplement accompanies our study of non-coding RNAs (ncRNAs) and their expression in 16 bat genomes. Firstly, we comprehensively annotated ncRNAs in the bat genomes and afterwards used our extended annotations for differential expression analyses. Within all investigated bat assemblies we annotated 667 ncRNA families including 162 snoRNAs and 193 miRNAs as well as rRNAs, tRNAs, several snRNAs and lncRNAs, and other structural ncRNA elements. We validated our ncRNA candidates by six RNA-Seq data sets and show significant expression patterns that have never been described before in a bat species on such a large scale. Between different bat families, we see differences in regard to their ncRNA reportoire and besides ncRNAs that are completely absent/present from certain bat groups, we see furhter differences in ncRNA copy numbers. This online supplement will be usable as a resource for deeper studying of bat evolution, ncRNAs repertoire, gene expression and regulation, ecology, and important host-virus interactions.

If you use our data please cite:
Nelly Mostajo Berrospi et al. "A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes" (2019), JOURNAL

How to work with this online supplement

In order to allow other scientists to work productively with this resource to answer their own questions regarding the expression of non-coding RNAs in bats, an explanation of how the supplement is structured and can be used can be found here.

General structure

On top of the online supplement page a list of content, divided in three main areas, is shown:

Under the heading "Data" you will first find important information on the bat genomes used and their assembly quality as well as information on the RNA-Seq data sets which will later be used for expression analysis. "Annotations" summarizes all ncRNA annotations divided by common ncRNA classes (miRNA, snoRNA, ...). Under this heading, also the final merged ncRNA annotations in GTF format (S11) can be found. These extended annotations can be downloaded and directly used as input for standard RNA-Seq analysis pipelines. Under the heading "RNA-Seq validation" you will find all differential expression comparisons performed on either 1) our novel ncRNA annotation, 2) our novel lncRNA annotation, or 3) the current NCBI annotation of non- and protein-coding genes.

Simply click on one of the links in the content list and the page will directly scroll to the corresponding entry. To navigate back to the content list, each supplemental entry has a "back to top" button located in the top right corner (or simply scroll the page).

Tables

The heart of this online supplement are interactive HTML tables presenting the annotated ncRNAs and their copy numbers for each bat species. These tables can be huge, due to the 16 bat genomes initially used to conduct this study and the vast amount of ncRNAs found for certain classes (e.g. 162 snoRNAs).

To allow a better handling of the tables, we implemented the following features:

Sortable columns
in the header line of each table, simply click on the arrow icon to sort the corresponding column (hold "shift" to sort multiple columns)
Foldout/slide option Table
per default, each table on the supplement page is shown, however, you can use the foldout icon on top of each table to hide certain tables
Foldout/slide option Download
on top of each table, you can find a foldout item to present download links for the table (CSV, EXCEL). All table content will be downloaded, not just the filtered entries.
Foldout/slide option Filter
open this foldout item to show different filter options for each table. Decide, by clicking the check boxes, which columns should be presented for each table. By this, you can select only a subset of the annotated bat species to be displayed.
Additional data
in addition, each table allows direct access to ncRNA class-specific output files such as nucleotide sequences in FASTA format, annotations in GFF and GTF (recommended) format and structural alignment files (STK)

All tables are sorted according to the phylogenetic relationship presented in the manuscript and the same color code is used in the filter item:

Screencast showing the table functionalities

This movie shows how to navigate and filter in tables of the online resource (please download the movie if it does not run in your browser):

Download (mov, 28MB)

Search

To search for a gene of interest simply use the browser functionalities ("control-f") and type a gene name or RFAM identifier. Or download the full GTF file for a bat (S11) and use local scripts to screen the annotation for your specific question.

Data, even more data...

All genome, annotation (GTF), and intermediate files can be additionally found in the Open Science Framework. Code to reproduce our analyses is available at GitHub.