Evolutionary characterization ofTy3/gypsy-like LTR retrotransposons in the parasitic cestodeEchinococcus granulosus

Abstract

Cyclophyllidean cestodes including Echinococcus granulosus have a smaller genome and show characteristics such as loss of the gut, a segmented body plan, and accelerated growth rate in hosts compared with other tissue-invading helminths. In an effort to address the molecular mechanism relevant to genome shrinkage, the evolutionary status of long-terminal-repeat (LTR) retrotransposons, which are known as the most potent genomic modulators, was investigated in the E. granulosus draft genome. A majority of the E. granulosus LTR retrotransposons were classified into a novel characteristic clade, named Saci-2, of the Ty3/gypsy family, while the remaining elements belonged to the CsRn1 clade of identical family. Their nucleotide sequences were heavily corrupted by frequent base substitutions and segmental losses. The ceased mobile activity of the major retrotransposons and the following intrinsic DNA loss in their inactive progenies might have contributed to decrease in genome size. Apart from the degenerate copies, a gag gene originating from a CsRn1-like element exhibited substantial evidences suggesting its domestication including a preserved coding profile and transcriptional activity, the presence of syntenic orthologues in cestodes, and selective pressure acting on the gene. To my knowledge, the endogenized gag gene is reported for the first time in invertebrates, though its biological function remains elusive.

Evidence for densovirus integrations into tapeworm genomes

“…This led to important questions on alternative mechanisms that are employed by parasitic flatworms to protect their genomes against transposons [11]. Cestode genomes contain a number of repeats with characteristics of transposable elements such as GYPSY class of LTR retrotransposons or Merlin DNA transposons [8, 16]. Furthermore, we recently identified a terminal repeat retrotransposon in miniature (TRIM) family which is massively expressed in germinative cells of taeniid cestodes [17].…”

“…This raises questions concerning alternative MGE silencing pathways in cestodes [11], which, to be properly addressed, first require the characterization of repetitive elements in their genomes. With the exception of a few reports on repetitive elements encoding spliced leader RNAs [14, 15], inactive copies of Gypsy class Long Terminal repeats [16], and stem cell-specifically expressed copies of a TRIM (terminal repeat retrotransposon in miniature)-element [17]; however, respective information is presently scarce.…”