Comparative transcriptomics across the prokaryotic tree of life

Ofir Cohen, Shany Doron, Omri Wurtzel, Daniel Dar, Sarit Edelheit, Iris Karunker, Eran Mick, Rotem Sorek*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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 5UTRs 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.

Original languageEnglish
Pages (from-to)W46-W53
JournalNucleic Acids Research
Issue numberW1
StatePublished - 2016
Externally publishedYes


FundersFunder number
Abisch–Frenkel foundation
ERC-StG program
Human Frontier Science ProgramRGP0011/2013
Leona M. and Harry B. Helmsley Charitable Trust
Seventh Framework Programme260432
Minerva Foundation
Deutsche Forschungsgemeinschaft711545


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