The eukaryotic ribosomal DNA (rDNA) cluster consists of multiple copies of three genes (18S, 5.8S, and 28S rDNA) and two internal transcribed spacers (ITS1 and ITS2). In recent years, an increasing number of rDNA sequence polymorphisms have been identified in numerous species. In the present study, we provide 33 complete ITS (ITS1-5.8S-ITS2) sequences from two Symphurus plagiusa individuals. To the best of our knowledge, these sequences are the first detailed information on ITS sequences in Pleuronectiformes. Here, two divergent types (Type A and B) of the ITS1-5.8S-ITS2 rDNA sequence were found, which mainly differ in sequence length, GC content, nucleotide diversity (π), secondary structure and minimum free energy. The ITS1-5.8S-ITS2 rDNA sequence of Type B was speculated to be a putative pseudogene according to pseudogene identification criteria. Cluster analysis showed that sequences from the same type clustered into one group and two major groups were formed. The high degree of ITS1-5.8S-ITS2 sequence polymorphism at the intra-specific level indicated that the S. plagiusa genome has evolved in a non-concerted evolutionary manner. These results not only provide useful data for ribosomal pseudogene identification, but also further contribute to the study of rDNA evolution in teleostean genomes.
BarguesM.D.ZuriagaM.A. & Mas-ComaS. (2014) Nuclear rDNA pseudogenes in Chagas disease vectors: evolutionary implications of a new 5.8S+ITS-2 paralogous sequence marker in triatomines of north, central and northern South America. Infect. Genet. Evol.21134-156.
ChowS.UenoY.ToyokawaM.OoharaI. & TakeyamaH. (2009) Preliminary analysis of length and GC content variation in the ribosomal first internal transcribed spacer (ITS1) of marine animals. Mar. Biotechnol.11301-306.
GongL.ShiW.YangM.SiL. & KongX. (2016a) Long duplication of 18S ribosomal DNA in Cynoglossus lineolatus (Pleuronectiformes: Cynoglossidae): novel molecular evidence for unequal crossing over model. Acta Oceanol. Sin.3538-50.
HarpkeD. & PetersonA. (2008a) Extensive 5.8 S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions. J. Plant Res.121261-270.
HoyM.S. & RodriguezR.J. (2013) Intragenomic sequence variation at the ITS1-ITS2 region and at the 18S and 28S nuclear ribosomal DNA genes of the New Zealand mud snail, Potamopyrgus antipodarum (Hydrobiidae: Mollusca). J. Molluscan Stud.79205-217.
KumarR.SinghM.KushwahaB.NagpureN.ManiI. & LakraW. (2013) Molecular characterization of major and minor rDNA repeats and genetic variability assessment in different species of mahseer found in north India. Gene527248-258.
LarkinM.A.BlackshieldsG.BrownN.P.ChennaR.McGettiganP.A.McWilliamH.ValentinF.WallaceI.M.WilmA.LopezR.ThompsonJ.D.GibsonT.J. & HigginsD.G. (2007) Clustal W and Clustal X version 2.0. Bioinformatics232947-2948.
RampersadS.N. (2014) ITS1, 5.8S and ITS2 secondary structure modelling for intra-specific differentiation among species of the Colletotrichum gloeosporioides sensu lato species complex. SpringerPlus3684.
SajdakS.L. & PhillipsR.B. (1997) Phylogenetic relationships among Coregonus species inferred from the DNA sequence of the first internal transcribed spacer (ITS1) of ribosomal DNA. Can. J. Fish. Aquat. Sci.541494-1503.
WeiderL.J.ElserJ.J.CreaseT.J.MateosM.CotnerJ.B. & MarkowT.A. (2005) The functional significance of ribosomal (r) DNA variation: impacts on the evolutionary ecology of organisms. Annu. Rev. Ecol. Evol. Syst.36219-242.
ZuriagaM.A.Mas-ComaS. & BarguesM.D. (2015) A nuclear ribosomal DNA pseudogene in triatomines opens a new research field of fundamental and applied implications in Chagas disease. Mem. Inst. Oswaldo Cruz110353-362.