Journal
ANNALS OF BOTANY
Volume 127, Issue 1, Pages 63-73Publisher
OXFORD UNIV PRESS
DOI: 10.1093/aob/mcaa169
Keywords
Camellia; ribosomal DNA; pseudogenes; concerted evolution; birth-and-death evolution
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Funding
- National Natural Science Foundation of China [31670223, 31270407]
- Key Research and Development Program of Guangdong Province [2018B0202020002]
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A high level of rDNA polymorphism exists universally in the genus Camellia, with functional rDNA being relatively conserved. Sequence variations mainly come from rRNA pseudogenes and GC-rich regions in the genome, indicating a mixture of concerted and birth-and-death evolution in Camellia.
Background and Aims The ribosomal DNA (rDNA) gene family, encoding ribosomal RNA (rRNA), has long been regarded as an archetypal example illustrating the model of concerted evolution. However, controversy is arising, as rDNA in many eukaryotic species has been proved to be polymorphic. Here, a metagenomic strategy was applied to detect the intragenomic polymorphism as well as the evolutionary patterns of 26S rDNA across the genus 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 favoured regions that are rich in GC. Specifically, some rRNA pseudogenes have existed in the genome for a long time, and have even experienced several expansion events, which has greatly enriched the abundance of rDNA polymorphism. Conclusions Camellia represents a group in which 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 structural stability through a methylation-induced process, and finally be eliminated from the genome.
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