Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny

作     者：Yurui Wang Chundi Wang Yaohan Jiang Laura A.Katz Feng Gao Ying Yan 

作者机构：Institute of Evolution & Marine Biodiversity Ocean University of China Key Laboratory of Mariculture Ocean University of China Ministry of Education Department of Biological Sciences Smith College 

出 版 物：《Science China(Life Sciences)》 (中国科学（生命科学英文版）)

年 卷 期：2019年第62卷第2期

页      面：203-214页

核心收录：

学科分类：0710[理学-生物学] 0830[工学-环境科学与工程（可授工学、理学、农学学位）] 07[理学] 071007[理学-遗传学] 

基　　金：supported by the National Natural Science Foundation of China (31772428) the National Science Foundation of the USA (1541511) Young Elite Scientists Sponsorship Program by CAST Fundamental Research Funds for the Central Universities (201841013 and 201762017) 

主　　题：ciliates SSU rDNA sequence variation phylogenetic analyses rDNA copy number ecological significance 

摘      要：Sequence-based approaches, such as analyses of ribosome DNA(rDNA) clone libraries and high-throughput amplicon sequencing, have been used extensively to infer evolutionary relationships and elucidate the biodiversity in microbial communities.However, recent studies demonstrate both r DNA copy number variation and intra-individual(intra-genomic) sequence variation in many organisms, which challenges the application of the rDNA-based surveys. In ciliates, an ecologically important clade of microbial eukaryotes, rDNA copy number and sequence variation are rarely studied. In the present study, we estimate the intraindividual small subunit rDNA(SSU r DNA) copy number and sequence variation in a wide range of taxa covering nine classes and 18 orders of the phylum Ciliophora. Our studies reveal that:(i) intra-individual sequence variation of SSU rDNA is ubiquitous in all groups of ciliates detected and the polymorphic level varies among taxa;(ii) there is a most common version of SSU rDNA sequence in each cell that is highly predominant and may represent the germline micronuclear template;(iii)compared with the most common version, other variant sequences differ in only 1–3 nucleotides, likely generated during macronuclear(somatic) amplification;(iv) the intra-cell sequence variation is unlikely to impact phylogenetic analyses;(v) the rDNA copy number in ciliates is highly variable, ranging from 103 to 106, with the highest record in Stentor roeselii. Overall,these analyses indicate the need for careful consideration of SSU r DNAvariation in analyses of the role of ciliates in ecosystems.