other MGEs

As a common class of transposable elements, long terminal repeat (LTR) retroelements play important roles in shaping the structures of their host genomes. The identification and genome-wide comparative analysis of LTR retroelements from multiple genomes are useful for a better understanding of the genome evolution.
We conducted a comprehensive de novo identification of LTR retroelements in the recently completed genome of Daphnia pulex, an aquatic microcrustacean. For the purpose of comparison, we conducted similar analyses on the completed genomes of four other invertebrate genomes, one fish genome, and one plant genome. In total, we identified 333 intact LTR retroelements in the D. pulex genome, which were categorized into 141 families. Nearly half of the identified intact elements were in the gypsy group. A large number of intact retroelements were also found in the copia (95), BEL/Pao (66) and DIRS (19) group. Polymorphism among mutation-accumulation lines indicates that some retroelements identified (two copia and two DIRS LTR retroelements) are dynamic in the genome of D. pulex. The sequences of these potentially active LTR retroelements have been deposited into Genbank [GenBank: EU528614-7]. The phylogenetic analysis of the representative reverse transcriptase sequences from all seven genomes showed that the retroelements in the D. pulex genome form distinct families of BEL/Pao, copia, gypsy and DIRS relative to those from other genomes examined, suggesting that a majority of the LTR retroelements in the D. pulex genome are novel.
The comprehensive phylogenetic analysis of newly identified LTR retroelements in the Daphnia genome reveals divergent lineages. In addition, transposon display experiments show that some of these retroelements may be active in current populations of D. pulex.

Table1. Summary of LTR retrotransposons in Daphnia
ClassSubfamilyIntact elementCopy numberTotal length(bp)