Dataset Information

The ecoresponsive genome of Daphnia pulex.

ABSTRACT: We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.

SUBMITTER: Colbourne JK

PROVIDER: S-EPMC3529199 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The ecoresponsive genome of Daphnia pulex.

Colbourne John K JK Pfrender Michael E ME Gilbert Donald D Thomas W Kelley WK Tucker Abraham A Oakley Todd H TH Tokishita Shinichi S Aerts Andrea A Arnold Georg J GJ Basu Malay Kumar MK Bauer Darren J DJ Cáceres Carla E CE Carmel Liran L Casola Claudio C Choi Jeong-Hyeon JH Detter John C JC Dong Qunfeng Q Dusheyko Serge S Eads Brian D BD Fröhlich Thomas T Geiler-Samerotte Kerry A KA Gerlach Daniel D Hatcher Phil P Jogdeo Sanjuro S Krijgsveld Jeroen J Kriventseva Evgenia V EV Kültz Dietmar D Laforsch Christian C Lindquist Erika E Lopez Jacqueline J Manak J Robert JR Muller Jean J Pangilinan Jasmyn J Patwardhan Rupali P RP Pitluck Samuel S Pritham Ellen J EJ Rechtsteiner Andreas A Rho Mina M Rogozin Igor B IB Sakarya Onur O Salamov Asaf A Schaack Sarah S Shapiro Harris H Shiga Yasuhiro Y Skalitzky Courtney C Smith Zachary Z Souvorov Alexander A Sung Way W Tang Zuojian Z Tsuchiya Dai D Tu Hank H Vos Harmjan H Wang Mei M Wolf Yuri I YI Yamagata Hideo H Yamada Takuji T Ye Yuzhen Y Shaw Joseph R JR Andrews Justen J Crease Teresa J TJ Tang Haixu H Lucas Susan M SM Robertson Hugh M HM Bork Peer P Koonin Eugene V EV Zdobnov Evgeny M EM Grigoriev Igor V IV Lynch Michael M Boore Jeffrey L JL

Science (New York, N.Y.) 20110201 6017

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that ...[more]

PMID: 21292972

Similar Datasets

Project description:Long terminal repeat (LTR) retroelements represent a successful group of transposable elements (TEs) that have played an important role in shaping the structure of many eukaryotic genomes. Here, we present a genome-wide analysis of LTR retroelements in Daphnia pulex, a cyclical parthenogen and the first crustacean for which the whole genomic sequence is available. In addition, we analyze transcriptional data and perform transposon display assays of lab-reared lineages and natural isolates to identify potential influences on TE mobility and differences in LTR retroelements loads among individuals reproducing with and without sex.We conducted a comprehensive de novo search for LTR retroelements and identified 333 intact LTR retroelements representing 142 families in the D. pulex genome. While nearly half of the identified LTR retroelements belong to the gypsy group, we also found copia (95), BEL/Pao (66) and DIRS (19) retroelements. Phylogenetic analysis of reverse transcriptase sequences showed that LTR retroelements in the D. pulex genome form many lineages distinct from known families, suggesting that the majority are novel. Our investigation of transcriptional activity of LTR retroelements using tiling array data obtained from three different experimental conditions found that 71 LTR retroelements are actively transcribed. Transposon display assays of mutation-accumulation lines showed evidence for putative somatic insertions for two DIRS retroelement families. Losses of presumably heterozygous insertions were observed in lineages in which selfing occurred, but never in asexuals, highlighting the potential impact of reproductive mode on TE abundance and distribution over time. The same two families were also assayed across natural isolates (both cyclical parthenogens and obligate asexuals) and there were more retroelements in populations capable of reproducing sexually for one of the two families assayed.Given the importance of LTR retroelements activity in the evolution of other genomes, this comprehensive survey provides insight into the potential impact of LTR retroelements on the genome of D. pulex, a cyclically parthenogenetic microcrustacean that has served as an ecological model for over a century.

Dataset Information

The ecoresponsive genome of Daphnia pulex.

Publications

The ecoresponsive genome of Daphnia pulex.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets