Details zur Publikation |
| Kategorie | Textpublikation |
| Referenztyp | Zeitschriften |
| DOI | 10.1002/jez.b.22560 |
| 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. |
| Quelle | Journal of Experimental Zoology Part B: Molecular and Developmental Evolution |
| Erscheinungsjahr | 2014 |
| Department | BIOTOX; PROTEOM |
| Band/Volume | 322 |
| Heft | 3 |
| Seite von | 177 |
| Seite bis | 189 |
| Sprache | englisch |
| 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. |
| dauerhafte UFZ-Verlinkung | https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=14621 |
| 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 10.1002/jez.b.22560 |
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