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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
A first Glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, Volume 322, No. 3, Year 2014
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Description
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 10Gb 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. © 2014 Wiley Periodicals, Inc.
Authors & Co-Authors
Rivarola-Duarte, Lorena
Germany, Leipzig
Helmholtz Zentrum Für Umweltforschung
Germany, Leipzig
Universität Leipzig
Otto, Christian
Germany, Leipzig
Universität Leipzig
Jühling, Frank
Germany, Leipzig
Universität Leipzig
Schreiber, Stephan
Germany, Leipzig
Helmholtz Zentrum Für Umweltforschung
Germany, Leipzig
Fraunhofer Institute for Cell Therapy and Immunology Izi
Bedulina, Daria
Russian Federation, Irkutsk
Irkutsk State University
Russian Federation, Irkutsk
Baikal Research Centre
Jakob, Lena
Germany, Bremerhaven
Alfred-wegener-institut Helmholtz-zentrum Für Polar- Und Meeresforschung
Gurkov, Anton
Russian Federation, Irkutsk
Irkutsk State University
Russian Federation, Irkutsk
Baikal Research Centre
Axenov-Gribanov, Denis
Russian Federation, Irkutsk
Irkutsk State University
Russian Federation, Irkutsk
Baikal Research Centre
Sahyoun, Abdullah H.
Germany, Leipzig
Universität Leipzig
Lebanon, Beirut
Université Libanaise
Lucassen, Magnus
Germany, Bremerhaven
Alfred-wegener-institut Helmholtz-zentrum Für Polar- Und Meeresforschung
Hackermüller, Jörg
Germany, Leipzig
Universität Leipzig
Germany, Leipzig
Helmholtz Zentrum Für Umweltforschung
Germany, Leipzig
Fraunhofer Institute for Cell Therapy and Immunology Izi
Hoffmann, Steve
Germany, Leipzig
Universität Leipzig
Sartoris, Franz
Germany, Bremerhaven
Alfred-wegener-institut Helmholtz-zentrum Für Polar- Und Meeresforschung
Pörtner, Hans-O.
Germany, Bremerhaven
Alfred-wegener-institut Helmholtz-zentrum Für Polar- Und Meeresforschung
Timofeyev, Maxim A.
Russian Federation, Irkutsk
Irkutsk State University
Russian Federation, Irkutsk
Baikal Research Centre
Luckenbach, Till
Germany, Leipzig
Helmholtz Zentrum Für Umweltforschung
Stadler, Peter F.
Germany, Leipzig
Universität Leipzig
Germany, Leipzig
Fraunhofer Institute for Cell Therapy and Immunology Izi
Germany, Leipzig
Max Planck Institute for Mathematics in the Sciences
Austria, Vienna
Universität Wien
Denmark, Copenhagen
Københavns Universitet
Mexico, Santa Fe, new
Santa fe Institute
Statistics
Citations: 31
Authors: 17
Affiliations: 11
Identifiers
Doi:
10.1002/jez.b.22560
ISSN:
15525007
e-ISSN:
15525015
Research Areas
Genetics And Genomics
Health System And Policy
Study Design
Cross Sectional Study
Study Approach
Quantitative