Rivarola-Duarte, L.L.Rivarola-DuarteOtto, C.C.OttoJühling, F.F.JühlingSchreiber, S.S.SchreiberBedulina, D.D.BedulinaJakob, L.L.JakobGurkov, A.A.GurkovAxenov-Gribanov, D.D.Axenov-GribanovSahyoun, A.H.A.H.SahyounLucassen, M.M.LucassenHackermüller, J.J.HackermüllerHoffmann, S.S.HoffmannSartoris, F.F.SartorisPörtner, H.-O.H.-O.PörtnerTimofeyev, M.M.TimofeyevLuckenbach, T.T.LuckenbachStadler, P.F.P.F.Stadler2022-03-042022-03-042014https://publica.fraunhofer.de/handle/publica/23686910.1002/jez.b.22560Eulimnogammarus 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.en572journal article