Abstract
BackgroundLong 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.ResultsWe 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.ConclusionsGiven 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.
Highlights
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
The definition of intact LTR retroelement was adapted from previous studies [3,18,19], and is limited to those that encode protein domains such as gag and pol and have pairs of LTRs at both ends
Transposable element dynamics in lab-reared lines and natural populations In order to assess the role of reproductive mode in retroelement distribution and abundance among sexually-and asexually-reproducing isolates, we developed a transposon display assay for two families of DIRS elements identified in the D. pulex genome
Summary
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. Transposable elements (TEs) have been found in most eukaryotic genomes and often constitute a significant portion of the genome (e.g., 80% of maize [1], 45% of human [2], and 5.3% of the fruit fly genome [3,4] are known to be comprised of TEs). Because they can transpose from one location to another within the genome or across genomes, the identification of TEs and analysis of their dynamics are important for a better understanding of the structure and evolution of both genomes and TEs themselves [5,6]. The identified LTRs can be combined with other important sequence features, including target site duplications (TSDs) and conserved protein domains, to identify intact
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