title: A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus.
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.
authors.affiliation: Department of Bioanalytical Ecotoxicology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany.
authors.forename: Lorena
authors.initials: L
authors.lastname: Rivarola-Duarte
authors.forename: Christian
authors.initials: C
authors.lastname: Otto
authors.forename: Frank
authors.initials: F
authors.lastname: Jühling
authors.forename: Stephan
authors.initials: S
authors.lastname: Schreiber
authors.forename: Daria
authors.initials: D
authors.lastname: Bedulina
authors.forename: Lena
authors.initials: L
authors.lastname: Jakob
authors.forename: Anton
authors.initials: A
authors.lastname: Gurkov
authors.forename: Denis
authors.initials: D
authors.lastname: Axenov-Gribanov
authors.forename: Abdullah H
authors.initials: AH
authors.lastname: Sahyoun
authors.forename: Magnus
authors.initials: M
authors.lastname: Lucassen
authors.forename: Jörg
authors.initials: J
authors.lastname: Hackermüller
authors.forename: Steve
authors.initials: S
authors.lastname: Hoffmann
authors.forename: Franz
authors.initials: F
authors.lastname: Sartoris
authors.forename: Hans-Otto
authors.initials: HO
authors.lastname: Pörtner
authors.forename: Maxim
authors.initials: M
authors.lastname: Timofeyev
authors.forename: Till
authors.initials: T
authors.lastname: Luckenbach
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D033304:Amphipoda / Q000235:genetics*; D000818:Animals; D005801:Genes, Homeobox; D059646:Genome Size; D054629:Genome, Mitochondrial; D017422:Sequence Analysis, DNA; D012800:Siberia