The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences

PLoS Genet. 2012;8(10):e1002984. doi: 10.1371/journal.pgen.1002984. Epub 2012 Oct 4.

Abstract

Insertions of parasitic DNA within coding sequences are usually deleterious and are generally counter-selected during evolution. Thanks to nuclear dimorphism, ciliates provide unique models to study the fate of such insertions. Their germline genome undergoes extensive rearrangements during development of a new somatic macronucleus from the germline micronucleus following sexual events. In Paramecium, these rearrangements include precise excision of unique-copy Internal Eliminated Sequences (IES) from the somatic DNA, requiring the activity of a domesticated piggyBac transposase, PiggyMac. We have sequenced Paramecium tetraurelia germline DNA, establishing a genome-wide catalogue of -45,000 IESs, in order to gain insight into their evolutionary origin and excision mechanism. We obtained direct evidence that PiggyMac is required for excision of all IESs. Homology with known P. tetraurelia Tc1/mariner transposons, described here, indicates that at least a fraction of IESs derive from these elements. Most IES insertions occurred before a recent whole-genome duplication that preceded diversification of the P. aurelia species complex, but IES invasion of the Paramecium genome appears to be an ongoing process. Once inserted, IESs decay rapidly by accumulation of deletions and point substitutions. Over 90% of the IESs are shorter than 150 bp and present a remarkable size distribution with a -10 bp periodicity, corresponding to the helical repeat of double-stranded DNA and suggesting DNA loop formation during assembly of a transpososome-like excision complex. IESs are equally frequent within and between coding sequences; however, excision is not 100% efficient and there is selective pressure against IES insertions, in particular within highly expressed genes. We discuss the possibility that ancient domestication of a piggyBac transposase favored subsequent propagation of transposons throughout the germline by allowing insertions in coding sequences, a fraction of the genome in which parasitic DNA is not usually tolerated.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Composition
  • Conserved Sequence
  • DNA Transposable Elements
  • DNA, Protozoan
  • Evolution, Molecular
  • Gene Dosage
  • Gene Order
  • Gene Rearrangement*
  • Genome, Protozoan*
  • Germ Cells*
  • INDEL Mutation
  • Models, Genetic
  • Molecular Sequence Data
  • Paramecium / genetics*
  • Selection, Genetic
  • Sequence Alignment

Substances

  • DNA Transposable Elements
  • DNA, Protozoan

Grant support

This work was supported by the ANR BLAN08-3_310945 “ParaDice,” the ANR 2010 BLAN 1603 “GENOMAC,” a CNRS ATIP-Plus grant to MB (2010–2011), and an “Equipe FRM” grant to EM. The sequencing was carried out at the Genoscope - Centre National de Séquençage (Convention GENOSCOPE-CEA number 128/AP 2007_2008/CNRS number 028666). CDW and AM were supported by Ph.D. fellowships from the Ministère de l'Enseignement Supérieur et de la Recherche. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.