Concerted and birth-and-death evolution of 26S ribosomal DNA in Camellia L.

BACKGROUND AND AIMS The Ribosomal DNA (rDNA) gene family, encoding ribosomal RNA (rRNA), has long be regarded as an archetypal example in illustrating the model of concerted evolution. However, controversy is arising, as rDNA within many eukaryotic species has been proved to be polymorphic. Here, a meta-genomic strategy was applied to detect the intra-genomic polymorphism as well as the evolutionary patterns of 26S rDNA across the genus of Camellia. METHODS Degenerate primer pairs were designed to amplify the 26S rDNA fragments from different Camellia species. The amplicons were then paired-end sequenced on the Illumina MiSeq platform. KEY RESULTS An extremely high level of rDNA polymorphism existed universally in Camellia. However, functional rDNA was still the major component of the family, and was relatively conserved among different Camellia species. Sequence variations mainly came from rRNA pseudogenes and favored regions which are rich in GC. Specifically, some rRNA pseudogenes have existed in the genome for a long time, and even experienced several periods of expansion, which has greatly enriched the abundance of rDNA polymorphism. CONCLUSIONS Camellia represents a group, where rDNA is subjected to a mixture of concerted and birth-and-death evolution. Some rRNA pseudogenes may still have potential functions. Conversely, when released from selection constraint, they can evolve in the direction of decreasing GC content and structure stability through a methylation induced process, and finally be eliminated from the genome.