Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/24105
Appears in Collections:Aquaculture Journal Articles
Peer Review Status: Refereed
Title: Genomewide comparison and novel ncRNAs of Aquificales
Authors: Lechner, Marcus
Nickel, Astrid I
Wehner, Stefanie
Riege, Konstantin
Wieseke, Nicolas
Beckmann, Benedikt M
Hartmann, Roland K
Manz, Manja
Contact Email: stefanie.wehner@stir.ac.uk
Keywords: Aquificales
Thermophiles
ncRNA
Aquificaceae
Desulfurobacteriaceae
Hydrogenothermaceae
Issue Date: 25-Jun-2014
Publisher: BioMed Central
Citation: Lechner M, Nickel AI, Wehner S, Riege K, Wieseke N, Beckmann BM, Hartmann RK & Manz M (2014) Genomewide comparison and novel ncRNAs of Aquificales, BMC Genomics, 15, Art. No.: 522.
Abstract: Background  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.  Results  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 severalin silicofeatures (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.  Conclusions  We have here re-analyzed the Aquificales, a group of bacteria thriving in extreme environments, sharing the feature of a small, compact genome with a reduced number of protein and ncRNA genes. We present several classical ncRNAs and riboswitch candidates. By combining in silico analysis with dRNA-seq data of A. aeolicus we predict nearly 100 novel ncRNA candidates.
Type: Journal Article
URI: http://hdl.handle.net/1893/24105
DOI Link: http://dx.doi.org/10.1186/1471-2164-15-522
Rights: © Lechner et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Affiliation: Philipps University of Marburg
Philipps University of Marburg
Aquaculture
Friedrich Schiller University of Jena
University Leipzig
Humboldt University Berlin
Philipps University of Marburg
Friedrich Schiller University of Jena

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