Publications - Published papers
Please find below publications of our group. Currently, we list 565 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (
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) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:webmaster@bioinf.uni-leipzig.de
©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.
A First Glimpse at the Genome of the Baikalian Amphipod (Eulimnogammarus verrucosus)
Lorena Rivarola-Duarte, Christian Otto, Frank Jühling, Stephan Schreiber, Daria Bedulina, Lena Jakob, Anton Gurkov, Denis Axenov-Gribanov, Abdullah H. Sahyoun, Magnus Lucassen, Jörg Hackermüller, Steve Hoffmann, Franz Sartoris, Hans-Otto Pörtner, Maxim Timofeyev, Till Luckenbach, Peter F. Stadler
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Status: Published
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, Volume 322, Issue 3, pages 177–189, May 2014,DOI: 10.1002/jez.b.22560
Abstract
Eulimnogammarus verrucosus is an amphipod endemic to the unique ecosystem of Lake Baikal and serves as an emerging model in ecotoxicological studies. We report here on a survey sequencing of its genome as a first step to establish sequence resources for this species. From a single lane of paired-end sequencing data we estimated the genome size as nearly 10 Gb and we obtained an overview of the repeat content. At least two thirds of the genome are non-unique DNA, and a third of the genomic DNA is composed of just five families of repetitive elements, including low-complexity sequences. Attempts to use off-the-shelf assembly tools failed on the available low-coverage data both before and after removal of highly repetitive components. Using a seed-based approach we nevertheless assembled short contigs covering 33 pre-microRNAs and the homeodomain-containing exon of nine Hox genes. The absence of clear evidence for paralogs implies that a genome duplication did not contribute to the large genome size. We furthermore report the assembly of the mitochondrial genome using a new, guided “crystallization” procedure. The initial results presented here set the stage for a more complete sequencing and analysis of this large genome.
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