GONG Li, SHI Wei, YANG Min, SI Lizhen, KONG Xiaoyu. Long duplication of 18S ribosomal DNA in Cynoglossus lineolatus (Pleuronectiformes: Cynoglossidae): novel molecular evidence for unequal crossing over model[J]. Acta Oceanologica Sinica, 2016, 35(12): 38-50. doi: 10.1007/s13131-016-0957-z
Citation: GONG Li, SHI Wei, YANG Min, SI Lizhen, KONG Xiaoyu. Long duplication of 18S ribosomal DNA in Cynoglossus lineolatus (Pleuronectiformes: Cynoglossidae): novel molecular evidence for unequal crossing over model[J]. Acta Oceanologica Sinica, 2016, 35(12): 38-50. doi: 10.1007/s13131-016-0957-z

Long duplication of 18S ribosomal DNA in Cynoglossus lineolatus (Pleuronectiformes: Cynoglossidae): novel molecular evidence for unequal crossing over model

doi: 10.1007/s13131-016-0957-z
  • Received Date: 2015-10-18
  • Rev Recd Date: 2016-05-13
  • Although 18S rDNA sequence is extremely conservative, the polymorphism still has been found in few species. In the present study, three types (Type A, B and C) of 18S rDNA sequence coexisted in Cynoglossus lineolatus genome, suggesting a non-concerted evolution process, rather than a strictly concerted evolution fashion. Based on the differences of sequence variation, GC content, secondary structure and minimum free energy, Types A and B were speculated as the potential pseudogenes. Additionally, a fascinating finding was a 189-bp duplication of 18S rDNA in Type A sequence. To our knowledge, this is the first report on such a long duplication in teleostean ribosomal DNA. Compared with several theories accounting for the formation of tandem repeats, the unequal crossing over model was thought to be the most likely mechanism to generate the 189-bp duplication of 18S rDNA. These results not only provide a novel molecular evidence for the unequal crossing over model, but also benefit for the further study on 18S rDNA in fishes.
  • loading
  • Alverson A J, Kolnick L. 2005. Intragenomic nucleotide polymorph-ism among small subunit (18S) rDNA paralogs in the diatom genus Skeletonema (Bacillariophyta). J Phycol, 41(6):1248-1257
    Bailey C D, Carr T G, Harris S A, et al. 2003. Characterization of angio-sperm nrDNA polymorphism, paralogy, and pseudogenes. Mol Phylogenet Evol, 29(3):435-455
    Benevolenskaya E V, Kogan G L, Tulin A V, et al. 1997. Segmented gene conversion as a mechanism of correction of 18S rRNA pseudogene located outside of rDNA cluster in D. melano-gaster. J Mol Evol, 44(6):646-651
    Benson G. 1999. Tandem repeats finder:a program to analyze DNA sequences. Nucleic Acids Res, 27(2):573-580
    Broughton R E, Dowling T E. 1994. Length variation in mitochondrial DNA of the minnow Cyprinella spiloptera. Genetics, 138(1):179-190
    Buroker N E, Brown J R, Gilbert T A, et al. 1990. Length heteroplasmy of sturgeon mitochondrial DNA:an illegitimate elongation model. Genetics, 124(1):157-163
    Carranza S, Giribet G, Ribera C, et al. 1996. Evidence that two types of 18S rDNA coexist in the genome of Dugesia (Schmidtea) medi-terranea (Platyhelminthes, Turbellaria, Tricladida). Mol Biol Evol, 13(6):824-832
    Chen Shanmin, Ma Kayan, Zeng Jin. 2011. Pseudogene:lessons from PCR bias, identification and resurrection. Mol Biol Rep, 38(6):3709-3715
    Chen Ziyi, Xiong Zhujun, Pan Xiaoyun, et al. 2015. Variation of gen-ome size and the ribosomal DNA ITS region of Alternanthera philoxeroides (Amaranthaceae) in Argentina, the USA, and China. J Syst Evol, 53(1):82-87
    Edwards Y J K, Elgar G, Clark M S, et al. 1998. The identification and characterization of microsatellites in the compact genome of the Japanese pufferfish, Fugu rubripes:perspectives in func-tional and comparative genomic analyses. J Mol Biol, 278(4):843-854
    Ellegren H. 2000. Microsatellite mutations in the germline:implica-tions for evolutionary inference. Trends Genet, 16(12):551-558
    Harpke D, Peterson A. 2007. Quantitative PCR revealed a minority of ITS copies to be functional in Mammillaria (Cactaceae). Int J Plant Sci, 168(8):1157-1160
    Harris D J, Crandall K A. 2000. Intragenomic variation within ITS1 and ITS2 of freshwater crayfishes (Decapoda:Cambaridae):im-plications for phylogenetic and microsatellite studies. Mol Biol Evol, 17(2):284-291
    Keller I, Chintauan-Marquier I C, Veltsos P, et al. 2006. Ribosomal DNA in the grasshopper Podisma pedestris:escape from con-certed evolution. Genetics, 174(2):863-874
    Krieger J, Hett A K, Fuerst P A, et al. 2006. Unusual intraindividual variation of the nuclear 18S rRNA gene is widespread within the Acipenseridae. J Hered, 97(3):218-225
    Kumar R, Singh M, Kushwaha B, et al. 2013. Molecular characteriza-tion of major and minor rDNA repeats and genetic variability assessment in different species of mahseer found in North In-dia. Gene, 527(1):248-258
    Larkin M A, Blackshields G, Brown N P, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics, 23(21):2947-2948
    Levinson G, Gutman G A. 1987. Slipped-strand mispairing:a major mechanism for DNA sequence evolution. Mol Biol Evol, 4(3):203-221
    Li Yi, Jiao Lei, Yao Yijian. 2013. Non-concerted ITS evolution in fungi, as revealed from the important medicinal fungus Ophiocordy-ceps sinensis. Mol Phylogenet Evol, 68(2):373-379
    Long E O, Dawid I B. 1980. Repeated genes in eukaryotes. Annu Rev Biochem, 49(1):727-764
    Melters D P, Bradnam K R, Young H A, et al. 2013. Comparative ana-lysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol, 14(1):R10
    Merlo M A, Cross I, Chairi H, et al. 2010. Analysis of three multigene families as useful tools in species characterization of two closely-related species, Dicentrarchus labrax, Dicentrarchus punctatus and their hybrids. Genes Genet Syst, 85(5):341-349
    Nyaku S T, Sripathi V R, Kantety R V, et al. 2013. Characterization of the two intra-individual sequence variants in the 18S rRNA gene in the plant parasitic Nematode, Rotylenchulus reniformis. PLoS One, 8(4):e60891
    Okada K, Yamazaki Y, Yokobori S, et al. 2010. Repetitive sequences in the lamprey mitochondrial DNA control region and speciation of Lethenteron. Gene, 465(1-2):45-52
    Platas G, Polishook J D, Peláez F. 2002. VNTR polymorphism in the ITS1 region (rDNA) in isolates of a Nodulisporium species. Mycol Res, 106(11):1293-1298
    Rouchka E C. 2010. Database of exact tandem repeats in the Zebrafish genome. BMC Genom, 11:347
    Santos S R, Kinzie Ⅲ R A, Sakai K, et al. 2003. Molecular characteriza-tion of nuclear small subunit (ISS)-rDNA pseudogenes in a symbiotic dinoflagellate (Symbiodinium, Dinophyta). J Euka-ryot Microbiol, 50(6):417-421
    Shi Wei, Kong Xiaoyu, Wang Zhongming, et al. 2013. Pause-melting misalignment:a novel model for the birth and motif indel of tandem repeats in the mitochondrial genome. BMC Genom, 14(1):103
    Smith G P. 1974. Unequal crossover and the evolution of multigene families. Cold Spring Harb Symp Quant Biol, 38:507-513
    Suzuki M T, Giovannoni S J. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Ap-pl Environ Microbol, 62(2):625-630
    Szostak J W, Wu R. 1980. Unequal crossing over in the ribosomal DNA of Saccharomyces cerevisiae. Nature, 284(5755):426-430
    Varadaraj K, Skinner D M. 1994. Denaturants or cosolvents improve the specificity of PCR amplification of a G + C-rich DNA using genetically engineered DNA polymerases. Gene, 140(1):1-5
    Waye J S, Willard H F. 1986. Molecular analysis of a deletion poly-morphism in alpha satellite of human chromosome 17:evid-ence for homologous unequal crossing-over and subsequent fixation. Nucleic Acids Res, 14(17):6915-6927
    Won H, Renner S S. 2005. The internal transcribed spacer of nuclear ribosomal DNA in the gymnosperm Gnetum. Mol Phylogenet Evol, 36(3):581-597
    Xu Jianpeng, Zhang Quanqi, Xu Xiaofei, et al. 2009. Intragenomic variability and pseudogenes of ribosomal DNA in Stone flounder Kareius bicoloratus. Mol Phylogenet Evol, 52(1):157-166
    Zhao Ying, Strope P K, Kozmin S G, et al. 2014. Structures of naturally evolved CUP1 tandem arrays in yeast indicate that these arrays are generated by unequal nonhomologous recombination. G3-Genes Genom Genet, 4(11):2259-2269
    Zuker M. 2003. Mfold web server for nucleic acid folding and hybrid-ization prediction. Nucleic Acids Res, 31(13):3406-3415
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Article Metrics

    Article views (936) PDF downloads(903) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return