J Syst Evol ›› 2018, Vol. 56 ›› Issue (3): 250-258.DOI: 10.1111/jse.12314

• Research Articles • Previous Articles    

An improved metagenomic strategy reveals an unprecedentedly high level of intragenomic polymorphism of ribosomal DNA in three species of Camellia

Yang Shao1†, Min Zhang1†, Ying Xu1,2, Yong-Qing Zhu3, Takahiro Yonezawa1, Yu-Guo Wang1, Zhi-Ping Song1, and Wen-Ju Zhang1*   

  1. 1Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai 200438, China 2Shanghai Railway Entry-Exit Inspection and Quarantine Bureau, Shanghai 200070, China 3Shanghai Institute of Planned Parenthood Research, Shanghai 200237, China Authors contributed equally to this work as first author.
  • Received:2018-01-20 Accepted:2018-03-13 Published:2018-05-10


The ribosomal DNA (rDNA) repeats of more and more species have been found to be polymorphic in the genome, and the understanding of this polymorphism is conducive not only to eliminating potential chaos in the metagenomic analysis (MGA), but also to providing rich information on rDNA evolution. In this study, the MGA previously used for the study of environmental microbial diversity was improved and extended to detect the intragenomic polymorphism (IGP) of rDNA in three species of Camellia L. The 3′‐end region of 26S rDNA of three individuals was amplified using degenerate primer pairs. Three annealing temperatures were applied to obtain as many ribotypes as possible, and equimolar amplicons from the three species were then pooled and sequenced using the Illumina MiSeq platform. An incredibly high level of IGP of rDNA was found in all three species. Nearly all of the ribotypes detected from this study were rDNA pseudogenes, and most of them have existed for a long time in the genome, with some generated from several rapid expansions. Our procedure provided an effective technique for detection of IGP of rDNA, and the particular evolutionary information of rDNAs in Camellia was also exploited.

Key words: 26S rDNA, Camellia, intra-genomic polymorphism, Miseq sequencing, pseudogene.