Rivarola-Duarte Lorena, Otto Christian, Jühling Frank, Schreiber Stephan, Bedulina Daria, Jakob Lena, Gurkov Anton, Axenov-Gribanov Denis, Sahyoun Abdullah H, Lucassen Magnus, Hackermüller Jörg, Hoffmann Steve, Sartoris Franz, Pörtner Hans-Otto, Timofeyev Maxim, Luckenbach Till, Stadler Peter F
Department of Bioanalytical Ecotoxicology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany.
J Exp Zool B Mol Dev Evol. 2014 May;322(3):177-89. doi: 10.1002/jez.b.22560. Epub 2014 Feb 12.
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.
疣背欧利摇蚊是一种双足节肢动物，为贝加尔湖独特生态系统所特有，是生态毒理学研究中的新兴模式生物。我们在此报告其基因组的调查测序情况，作为为该物种建立序列资源的第一步。从单条双末端测序数据通道中，我们估计基因组大小接近10Gb，并获得了重复序列含量的概况。基因组中至少三分之二是非独特DNA，基因组DNA的三分之一仅由五个重复元件家族组成，包括低复杂性序列。在去除高度重复成分之前和之后尝试使用现成的组装工具对可用的低覆盖数据均告失败。不过，我们采用基于种子的方法组装了短重叠群，覆盖了33个前体微小RNA和9个Hox基因含同源异型结构域的外显子。没有明显的旁系同源物证据表明基因组加倍并非导致大基因组大小的原因。我们还报告了使用一种新的、有指导的“结晶”程序组装线粒体基因组的情况。此处展示的初步结果为更完整地测序和分析这个大基因组奠定了基础。
