Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

Abstract

Ciliates are unicellular eukaryotes with both a germline genome and a somatic genome in the same cytoplasm. The somatic macronucleus (MAC), responsible for gene expression, is not sexually transmitted but develops from a copy of the germline micronucleus (MIC) at each sexual generation. In the MIC genome of Paramecium tetraurelia, genes are interrupted by tens of thousands of unique intervening sequences called internal eliminated sequences (IESs), which have to be precisely excised during the development of the new MAC to restore functional genes. To understand the evolutionary origin of this peculiar genomic architecture, we sequenced the MIC genomes of 9 Paramecium species (from approximately 100 Mb in Paramecium aurelia species to >1.5 Gb in Paramecium caudatum). We detected several waves of IES gains, both in ancestral and in more recent lineages. While the vast majority of IESs are single copy in present-day genomes, we identified several families of mobile IESs, including nonautonomous elements acquired via horizontal transfer, which generated tens to thousands of new copies. These observations provide the first direct evidence that transposable elements can account for the massive proliferation of IESs in Paramecium. The comparison of IESs of different evolutionary ages indicates that, over time, IESs shorten and diverge rapidly in sequence while they acquire features that allow them to be more efficiently excised. We nevertheless identified rare cases of IESs that are under strong purifying selection across the aurelia clade. The cases examined contain or overlap cellular genes that are inactivated by excision during development, suggesting conserved regulatory mechanisms. Similar to the evolution of introns in eukaryotes, the evolution of Paramecium IESs highlights the major role played by selfish genetic elements in shaping the complexity of genome architecture and gene expression.

Transposon debris in ciliate genomes

“…A study published in the current issue of PLOS Biology [ 3 ] provides evidence to support a model proposed by Klobutcher and Herrick in 1997 that linked the origin of IESs to transposable elements (TEs) in ciliate genomes [ 4 ]. TEs play a key role in genome rearrangement in other cells and are occasionally domesticated by the host.…”

“…While this model may explain the origin of IESs, there has been mostly indirect evidence to support it (e.g., the resemblance of sequences flanking IESs to TE target site motifs [ 10 ]). Sellis and colleagues provide compelling evidence that thousands of IESs derive from TEs by using comparative genomics within the Paramecium genus [ 3 ].…”

“…In this study, Sellis and colleagues annotated and dated IESs in 9 diverse species of Paramecium [ 3 ]. They sequenced both genomes in each species and annotated IESs by comparing short MIC reads to the MAC genome assemblies.…”

“…Older IESs are much shorter, compatible with the “fade” step of the model. Moreover, some conserved IESs encode MIC-limited genes [ 3 , 12 ] or provide a “switch” to regulate gene expression.…”

“…Old IESs are less often under epigenetic control than new ones [3]. In P. tetraurelia, 70% of IESs require histone methylation or small RNAs for removal, while the rest are independent of either pathway [11].…”