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 in particular 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.

Evolution of mitochondrial genomes in Baikalian amphipods

“…in length and including those of E.verrucosus [71] were predicted for the analysis (Additional file 6). Most of the predicted tRNAs possess the expected clover-leaf structures, however some of them have aberrant structures.…”

“…[104] and E.verrucosus (473 b.p.) [71] and also in the mitochondrial genome of G. duebeni [44] (Fig. 1, Additional file 3).…”

The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion

“…A growing number of transcriptomes for larger phylogenetic analyses have led to differing hypotheses of the relationships of the major pancrustacean groups (Figure 1B) (Meusemann et al, 2010; Regier et al, 2010; Oakley et al, 2013; von Reumont et al, 2012). The genome of the amphipod crustacean Parhyale hawaiensis addresses the paucity of high quality non-hexapod genomes among the pancrustacean group, and will help to resolve relationships within this group as more genomes and complete proteomes become available (Rivarola-Duarte et al, 2014; Kenny et al, 2014). Crucially, genome sequence data is also necessary to further advance research in Parhyale , currently the most tractable crustacean model system.…”

Candidate pathogenicity islands in the genome of ‘CandidatusRickettsiella isopodorum’, an intracellular bacterium infecting terrestrial isopod crustaceans

“…To ameliorate this problem, we developed a custom pipeline for an iterative mapping-and-assembly strategy, somewhat similar to approaches used by others to assemble mitochondrial genomes from whole genomic DNA (Hahn, Bachmann & Chevreux, 2013; Rivarola-Duarte et al, 2014; Chandler et al, 2015). We first divided the contigs into two sets, representing each strain of Rickettsiella , based on sequence coverage in the two DNA samples, as partitioning them based on homology to R. grylli NZ_AAQJ00000000 alone seemed to mis-classify a few contigs (Fig.…”