Details zur Publikation

Referenztyp Zeitschriften
DOI / URL Link
Titel (primär) A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus
Autor Rivarola-Duarte, L.; Otto, C.; Jühling, F.; Schreiber, S.; Bedulina, D.S.; Jakob, L.; Gurkov, A.; Axenov-Gribanov, D.; Sahyoun, A.H.; Lucassen, M.; Hackermüller, J.; Hoffmann, S.; Sartoris, F.; Pörtner, H.-O.; Timofeyev, M.; Luckenbach, T.; Stadler, P.F.;
Journal / Serie Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
Erscheinungsjahr 2014
Band/Volume 322
Heft 3
Sprache englisch;
POF III (gesamt) T32;
UFZ Querschnittsthemen RU2
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.
ID 14621
dauerhafte UFZ-Verlinkung
Rivarola-Duarte, L., Otto, C., Jühling, F., Schreiber, S., Bedulina, D.S., Jakob, L., Gurkov, A., Axenov-Gribanov, D., Sahyoun, A.H., Lucassen, M., Hackermüller, J., Hoffmann, S., Sartoris, F., Pörtner, H.-O., Timofeyev, M., Luckenbach, T., Stadler, P.F. (2014):
A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus
J. Exp. Zool. Part B 322 (3), 177 - 189