Global trends of whole-genome duplications revealed by the ciliate

The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints. Ciliates are unique among unicellular organisms in that they separate germline and somatic functions 1. Each cell harbours two kinds of nucleus, namely silent diploid micronuclei and highly polyploid macronuclei. The latter are unusual in that they contain an exten­ sively rearranged genome streamlined for expression and divide by a non-mitotic process. Only micronuclei undergo meiosis to perpetu­ ate genetic information; the macronuclei are lost at each sexual gen­ eration and develop anew from the micronuclear lineage. In Paramecillm the exact number of micronuclear chromosomes (more than 50) and the structures oftheir centromeres and telomeres remain unknown. During macronuclear development, these chro­ mosomes are amplified to about 800 copies and undergo two types of DNA elimination event. Tens of thousand of short, unique copy elements (internal eliminated sequences) are removed by a precise mechanism that leads to the reconstitution of functional genes 2 • Transposable elements and other repeated sequences are removed by an imprecise mechanism leading either to chromosome frag­ mentation and de novo telomere addition or to variable internal deletions'. These rearrangements occur after a few rounds of endoreplication, leading to some heterogeneity in the sequences abutting the imprecisely eliminated regions'. The sizes of the result­ ing' acentric macronuclear chromosomes range from 50-1,000 kilobases (kb) as measured by pulsed-field gel electrophoresis. Because the sexual process of autogamy results in an entirely homozygous genotype', the macronuclear DNA that was sequenced was genetic­ ally homogeneous.