Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Research article

Genomewide comparison and novel ncRNAs of Aquificales

Marcus Lechner, Astrid I Nickel, Stefanie Wehner, Konstantin Riege, Nicolas Wieseke, Benedikt M Beckmann, Roland K Hartmann and Manja Marz

Author Affiliations

For all author emails, please log on.

BMC Genomics 2014, 15:522  doi:10.1186/1471-2164-15-522

Published: 25 June 2014

Abstract (provisional)

The Aquificales are a diverse group of thermophilic bacteria that thrive in terrestrial and marine hydrothermal environments. They can be divided into the families Aquificaceae, Desulfurobacteriaceae and Hydrogenothermaceae. Although eleven fully sequenced and assembled genomes are available, only little is known about this taxonomic order in terms of RNA metabolism. In this work, we compare the available genomes, extend their protein annotation, identify regulatory sequences, annotate non-coding RNAs (ncRNAs) of known function, predict novel ncRNA candidates, show idiosyncrasies of the genetic decoding machinery, present two different types of transfer-messenger RNAs and variations of the CRISPR systems. Furthermore, we performed a phylogenetic analysis of the Aquificales based on entire genome sequences, and extended this by a classification among all bacteria using 16S rRNA sequences and a set of orthologous proteins. Combining several in silico features (e.g. conserved and stable secondary structures, GC-content, comparison based on multiple genome alignments) with an in vivo dRNA-seq transcriptome analysis of Aquifex aeolicus , we predict roughly 100 novel ncRNA candidates in this bacterium.

The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.