A first Glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus
Identifieur interne : 001E30 ( Main/Exploration ); précédent : 001E29; suivant : 001E31A first Glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus
Auteurs : Lorena Rivarola-Duarte [Allemagne] ; Christian Otto [Allemagne] ; Frank Jühling [Allemagne] ; Stephan Schreiber [Allemagne] ; Daria Bedulina [Russie] ; Lena Jakob [Allemagne] ; Anton Gurkov [Russie] ; Denis Axenov-Gribanov [Russie] ; Abdullah H. Sahyoun [Allemagne, Liban] ; Magnus Lucassen [Allemagne] ; Jörg Hackermüller [Allemagne] ; Steve Hoffmann [Allemagne] ; Franz Sartoris [Allemagne] ; Hans-Otto Pörtner [Allemagne] ; Maxim Timofeyev [Russie, Allemagne] ; Till Luckenbach [Allemagne] ; Peter F. Stadler [Allemagne, Autriche, Danemark, États-Unis]Source :
- Journal of Experimental Zoology Part B: Molecular and Developmental Evolution [ 1552-5007 ] ; 2014-05.
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. J. Exp. Zool. (Mol. Dev. Evol.) 322B: 177–189, 2014. © 2014 Wiley Periodicals, Inc.
Url:
DOI: 10.1002/jez.b.22560
Affiliations:
- Allemagne, Autriche, Danemark, Liban, Russie, États-Unis
- District de Leipzig, Nouveau-Mexique, Saxe (Land), Vienne (Autriche)
- Leipzig, Vienne (Autriche)
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: 000221
- to stream Istex, to step Curation: 000221
- to stream Istex, to step Checkpoint: 000214
- to stream Main, to step Merge: 001E45
- to stream Main, to step Curation: 001E30
Le document en format XML
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Irkutsk</wicri:regionArea><wicri:noRegion>Irkutsk</wicri:noRegion></affiliation><affiliation></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Allemagne</country></affiliation></author><author><name sortKey="Luckenbach, Till" sort="Luckenbach, Till" uniqKey="Luckenbach T" first="Till" last="Luckenbach">Till Luckenbach</name><affiliation wicri:level="3"><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Bioanalytical Ecotoxicology, UFZ—Helmholtz Centre for Environmental Research, Leipzig</wicri:regionArea><placeName><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Leipzig</region><settlement type="city">Leipzig</settlement></placeName></affiliation><affiliation></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Allemagne</country></affiliation></author><author><name sortKey="Stadler, Peter F" sort="Stadler, Peter F" uniqKey="Stadler P" first="Peter F." last="Stadler">Peter F. Stadler</name><affiliation wicri:level="3"><country xml:lang="fr">Allemagne</country><wicri:regionArea>Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig</wicri:regionArea><placeName><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Leipzig</region><settlement type="city">Leipzig</settlement></placeName></affiliation><affiliation wicri:level="3"><country xml:lang="fr">Allemagne</country><wicri:regionArea>LIFE, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig</wicri:regionArea><placeName><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Leipzig</region><settlement type="city">Leipzig</settlement></placeName></affiliation><affiliation wicri:level="3"><country xml:lang="fr">Allemagne</country><wicri:regionArea>Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig</wicri:regionArea><placeName><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Leipzig</region><settlement type="city">Leipzig</settlement></placeName></affiliation><affiliation wicri:level="3"><country xml:lang="fr">Allemagne</country><wicri:regionArea>RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Leipzig</wicri:regionArea><placeName><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Leipzig</region><settlement type="city">Leipzig</settlement></placeName></affiliation><affiliation wicri:level="3"><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Mathematics in the Sciences, Leipzig</wicri:regionArea><placeName><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Leipzig</region><settlement type="city">Leipzig</settlement></placeName></affiliation><affiliation wicri:level="3"><country xml:lang="fr">Autriche</country><wicri:regionArea>Department of Theoretical Chemistry, University of Vienna, Wien</wicri:regionArea><placeName><settlement type="city">Vienne (Autriche)</settlement><region nuts="2" type="province">Vienne (Autriche)</region></placeName></affiliation><affiliation wicri:level="1"><country xml:lang="fr">Danemark</country><wicri:regionArea>Center for Non‐Coding RNA in Technology and Health, University of Copenhagen, Frederiksberg</wicri:regionArea><wicri:noRegion>Frederiksberg</wicri:noRegion></affiliation><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><placeName><region type="state">Nouveau-Mexique</region></placeName><wicri:cityArea>Santa Fe Institute, Santa Fe</wicri:cityArea></affiliation><affiliation></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Allemagne</country></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</title><title level="j" type="alt">JOURNAL OF EXPERIMENTAL ZOOLOGY PART B: MOLECULAR AND DEVELOPMENTAL EVOLUTION</title><idno type="ISSN">1552-5007</idno><idno type="eISSN">1552-5015</idno><imprint><biblScope unit="vol">322</biblScope><biblScope unit="issue">3</biblScope><biblScope unit="page" from="177">177</biblScope><biblScope unit="page" to="189">189</biblScope><biblScope unit="page-count">13</biblScope><date type="published" when="2014-05">2014-05</date></imprint><idno type="ISSN">1552-5007</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1552-5007</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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. J. Exp. Zool. (Mol. Dev. Evol.) 322B: 177–189, 2014. © 2014 Wiley Periodicals, Inc.</div></front></TEI><affiliations><list><country><li>Allemagne</li><li>Autriche</li><li>Danemark</li><li>Liban</li><li>Russie</li><li>États-Unis</li></country><region><li>District de Leipzig</li><li>Nouveau-Mexique</li><li>Saxe (Land)</li><li>Vienne (Autriche)</li></region><settlement><li>Leipzig</li><li>Vienne (Autriche)</li></settlement></list><tree><country name="Allemagne"><region name="Saxe (Land)"><name sortKey="Rivarola Uarte, Lorena" sort="Rivarola Uarte, Lorena" uniqKey="Rivarola Uarte L" first="Lorena" last="Rivarola-Duarte">Lorena Rivarola-Duarte</name></region><name sortKey="Hackermuller, Jorg" sort="Hackermuller, Jorg" uniqKey="Hackermuller J" first="Jörg" last="Hackermüller">Jörg Hackermüller</name><name sortKey="Hackermuller, Jorg" sort="Hackermuller, Jorg" uniqKey="Hackermuller J" first="Jörg" last="Hackermüller">Jörg Hackermüller</name><name sortKey="Hackermuller, Jorg" sort="Hackermuller, Jorg" uniqKey="Hackermuller J" first="Jörg" last="Hackermüller">Jörg Hackermüller</name><name sortKey="Hoffmann, Steve" sort="Hoffmann, Steve" uniqKey="Hoffmann S" first="Steve" last="Hoffmann">Steve Hoffmann</name><name sortKey="Hoffmann, Steve" sort="Hoffmann, Steve" uniqKey="Hoffmann S" first="Steve" last="Hoffmann">Steve Hoffmann</name><name sortKey="Jakob, Lena" sort="Jakob, Lena" uniqKey="Jakob L" first="Lena" last="Jakob">Lena Jakob</name><name sortKey="Juhling, Frank" sort="Juhling, Frank" uniqKey="Juhling F" first="Frank" last="Jühling">Frank Jühling</name><name sortKey="Lucassen, Magnus" sort="Lucassen, Magnus" uniqKey="Lucassen M" first="Magnus" last="Lucassen">Magnus Lucassen</name><name sortKey="Luckenbach, Till" sort="Luckenbach, Till" uniqKey="Luckenbach T" first="Till" last="Luckenbach">Till Luckenbach</name><name sortKey="Luckenbach, Till" sort="Luckenbach, Till" uniqKey="Luckenbach T" first="Till" last="Luckenbach">Till Luckenbach</name><name sortKey="Otto, Christian" sort="Otto, Christian" uniqKey="Otto C" first="Christian" last="Otto">Christian Otto</name><name sortKey="Otto, Christian" sort="Otto, Christian" uniqKey="Otto C" first="Christian" last="Otto">Christian Otto</name><name sortKey="Otto, Christian" sort="Otto, Christian" uniqKey="Otto C" first="Christian" last="Otto">Christian Otto</name><name sortKey="Portner, Hans Tto" sort="Portner, Hans Tto" uniqKey="Portner H" first="Hans-Otto" last="Pörtner">Hans-Otto Pörtner</name><name sortKey="Portner, Hans Tto" sort="Portner, Hans Tto" uniqKey="Portner H" first="Hans-Otto" last="Pörtner">Hans-Otto Pörtner</name><name sortKey="Rivarola Uarte, Lorena" sort="Rivarola Uarte, Lorena" uniqKey="Rivarola Uarte L" first="Lorena" last="Rivarola-Duarte">Lorena Rivarola-Duarte</name><name sortKey="Sahyoun, Abdullah H" sort="Sahyoun, Abdullah H" uniqKey="Sahyoun A" first="Abdullah H." last="Sahyoun">Abdullah H. Sahyoun</name><name sortKey="Sartoris, Franz" sort="Sartoris, Franz" uniqKey="Sartoris F" first="Franz" last="Sartoris">Franz Sartoris</name><name sortKey="Schreiber, Stephan" sort="Schreiber, Stephan" uniqKey="Schreiber S" first="Stephan" last="Schreiber">Stephan Schreiber</name><name sortKey="Schreiber, Stephan" sort="Schreiber, Stephan" uniqKey="Schreiber S" first="Stephan" last="Schreiber">Stephan Schreiber</name><name sortKey="Stadler, Peter F" sort="Stadler, Peter F" uniqKey="Stadler P" first="Peter F." last="Stadler">Peter F. Stadler</name><name sortKey="Stadler, Peter F" sort="Stadler, Peter F" uniqKey="Stadler P" first="Peter F." last="Stadler">Peter F. Stadler</name><name sortKey="Stadler, Peter F" sort="Stadler, Peter F" uniqKey="Stadler P" first="Peter F." last="Stadler">Peter F. Stadler</name><name sortKey="Stadler, Peter F" sort="Stadler, Peter F" uniqKey="Stadler P" first="Peter F." last="Stadler">Peter F. Stadler</name><name sortKey="Stadler, Peter F" sort="Stadler, Peter F" uniqKey="Stadler P" first="Peter F." last="Stadler">Peter F. Stadler</name><name sortKey="Stadler, Peter F" sort="Stadler, Peter F" uniqKey="Stadler P" first="Peter F." last="Stadler">Peter F. Stadler</name><name sortKey="Timofeyev, Maxim" sort="Timofeyev, Maxim" uniqKey="Timofeyev M" first="Maxim" last="Timofeyev">Maxim Timofeyev</name></country><country name="Russie"><noRegion><name sortKey="Bedulina, Daria" sort="Bedulina, Daria" uniqKey="Bedulina D" first="Daria" last="Bedulina">Daria Bedulina</name></noRegion><name sortKey="Axenov Ribanov, Denis" sort="Axenov Ribanov, Denis" uniqKey="Axenov Ribanov D" first="Denis" last="Axenov-Gribanov">Denis Axenov-Gribanov</name><name sortKey="Axenov Ribanov, Denis" sort="Axenov Ribanov, Denis" uniqKey="Axenov Ribanov D" first="Denis" last="Axenov-Gribanov">Denis Axenov-Gribanov</name><name sortKey="Bedulina, Daria" sort="Bedulina, Daria" uniqKey="Bedulina D" first="Daria" last="Bedulina">Daria Bedulina</name><name sortKey="Gurkov, Anton" sort="Gurkov, Anton" uniqKey="Gurkov A" first="Anton" last="Gurkov">Anton Gurkov</name><name sortKey="Gurkov, Anton" sort="Gurkov, Anton" uniqKey="Gurkov A" first="Anton" last="Gurkov">Anton Gurkov</name><name sortKey="Timofeyev, Maxim" sort="Timofeyev, Maxim" uniqKey="Timofeyev M" first="Maxim" last="Timofeyev">Maxim Timofeyev</name><name sortKey="Timofeyev, Maxim" sort="Timofeyev, Maxim" uniqKey="Timofeyev M" first="Maxim" last="Timofeyev">Maxim Timofeyev</name></country><country name="Liban"><noRegion><name sortKey="Sahyoun, Abdullah H" sort="Sahyoun, Abdullah H" uniqKey="Sahyoun A" first="Abdullah H." last="Sahyoun">Abdullah H. Sahyoun</name></noRegion></country><country name="Autriche"><region name="Vienne (Autriche)"><name sortKey="Stadler, Peter F" sort="Stadler, Peter F" uniqKey="Stadler P" first="Peter F." last="Stadler">Peter F. Stadler</name></region></country><country name="Danemark"><noRegion><name sortKey="Stadler, Peter F" sort="Stadler, Peter F" uniqKey="Stadler P" first="Peter F." last="Stadler">Peter F. Stadler</name></noRegion></country><country name="États-Unis"><region name="Nouveau-Mexique"><name sortKey="Stadler, Peter F" sort="Stadler, Peter F" uniqKey="Stadler P" first="Peter F." last="Stadler">Peter F. Stadler</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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