Comparative transcriptomics across the prokaryotic tree of life
Ofir Cohen1,2, Shany Doron1, Omri Wurtzel1,3, Daniel Dar1, Sarit Edelheit1, Iris Karunker1, Eran Mick1,4 and Rotem Sorek1,*
- Author Affiliations
1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
2Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
3Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
4Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
↵*To whom correspondence should be addressed. Tel: +1 972 8 934 6342; Fax: +1 972 8 934 4108; Email: rotem.sorek@weizmann.ac.il
Received February 8, 2016. Revision received April 20, 2016. Accepted April 28, 2016.
Abstract
Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis-antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of non-coding RNAs in a given organism is challenging, especially since some of these RNAs were attributed to ‘transcriptional noise’. To allow the search for conserved transcriptomic elements we produced comparative transcriptome maps for multiple species across the microbial tree of life. These transcriptome maps are detailed in annotations, comparable by gene families, and BLAST-searchable by user provided sequences. Our transcriptome collection includes 18 model organisms spanning 10 phyla/subphyla of bacteria and archaea that were sequenced using standardized RNA-seq methods. The utility of the comparative approach, as implemented in our web server, is demonstrated by highlighting genes with exceptionally long 5′UTRs across species, which correspond to many known riboswitches and further suggest novel putative regulatory elements. Our study provides a standardized reference transcriptome to major clinically and environmentally important microbial phyla. The viewer is available at http://exploration.weizmann.ac.il/TCOL, setting a framework for comparative studies of the microbial non-coding genome.
© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
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