A first Glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus


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Hans.Poertner [ at ] awi.de

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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Scopus/ISI peer-reviewed
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Published
Eprint ID
35962
DOI 10.1002/jez.b.22560

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Rivarola-Duarte, L. , Otto, C. , Jühling, F. , Schreiber, S. , Bedulina, D. , Jakob, L. , Gurkov, A. , Axenov-Gribanov, D. , Sahyoun, A. H. , Lucassen, M. , Hackermüller, J. , Hoffmann, S. , Sartoris, F. J. , Pörtner, H. O. , Timofeyev, M. , Luckenbach, T. and Stadler, P. F. (2014): A first Glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus , Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 322 (3), pp. 177-189 . doi: 10.1002/jez.b.22560


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