Premium
An improved metagenomic strategy reveals an unprecedentedly high level of intragenomic polymorphism of ribosomal DNA in three species of Camellia
Author(s) -
Shao Yang,
Zhang Min,
Xu Ying,
Zhu YongQing,
Yonezawa Takahiro,
Wang YuGuo,
Song ZhiPing,
Zhang WenJu
Publication year - 2018
Publication title -
journal of systematics and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.249
H-Index - 46
eISSN - 1759-6831
pISSN - 1674-4918
DOI - 10.1111/jse.12314
Subject(s) - biology , pseudogene , ribosomal dna , metagenomics , genome , amplicon , genetics , ribosomal rna , evolutionary biology , gene , polymerase chain reaction , phylogenetics
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.