Abstract
Length and guanine–cytosine (GC) content of the ribosomal first internal transcribed spacer (ITS1) were compared across a wide variety of marine animal species, and its phylogenetic utility was investigated. From a total of 773 individuals representing 599 species, we only failed to amplify the ITS1 sequence from 87 individuals by polymerase chain reaction with universal ITS1 primers. No species was found to have an ITS1 region shorter than 100 bp. In general, the ITS1 sequences of vertebrates were longer (318 to 2,318 bp) and richer in GC content (56.8% to 78%) than those of invertebrates (117 to 1,613 bp and 35.8% to 71.3%, respectively). Specifically, gelatinous animals (Cnidaria and Ctenophora) were observed to have short ITS1 sequences (118 to 422 bp) with lower GC content (35.8% to 61.7%) than the other animal taxa. Mollusca and Crustacea were diverse groups with respect to ITS1 length, ranging from 108 to 1,118 and 182 to 1,613 bp, respectively. No universal relationship between length and GC content was observed. Our data indicated that ITS1 has a limited utility for phylogenetic analysis as obtaining confident sequence alignment was often impossible between different genera of the same family and even between congeneric species.
This is a preview of subscription content, log in via an institution to check access.
References
Chu KH, Li CP, Ho HY (2001) The first internal transcribed spacer (ITS-1) of ribosomal DNA as a molecular marker for phylogenetic and population analyses in crustacean. Mar Biotechnol 3:335–361
Coleman AW, Vacquier VD (2004) Exploring the phylogenetic utility of ITS sequences for animals: a test case for abalone (Haliotis). J Mol Evol 54:246–257
Croce O, Lamarre M, Christen R (2006) Querying the public databases for sequences using complex keywords contained in the feature lines. BMC Bioinformatics 7:45–50
Dover GA (1986) Molecular drive in multigene families, how biological novelties arise, spread and are assimilated. Trends Genet 2:159–165
Furlong JC, Maden BE (1983) Patterns of major divergence between the internal transcribed spacers of ribosomal DNA in Xenopus borealis and Xenopus laevis, and of minimal divergence within ribosomal coding regions. EMBO J 2:443–448
Goldman WE, Goldberg G, Bowman LH, Steinmetz D, Schlessinger D (1983) Mouse rDNA: sequences and evolutionary analysis of spacer and mature RNA regions. Mol Cell Biol 3:1488–1500
Gonzalez IL, Sylvester JE, Smith TF, Stambolian D, Schmickel RD (1990) Ribosomal RNA gene sequences and hominoid phylogeny. Mol Biol Evol 7:203–219
Gottschling M, Plötner J (2004) Secondary structure models of the nuclear internal transcribed spacer regions and 5.8S rRNA in Calciodinelloideae (Peridiniaceae) and other dinoflagellates. Nucleic Acids Res 32:307–315
Hall LMC, Maden BEH (1980) Nucleotide sequence through the 18S-28S intergene region of a vertebrate ribosomal transcription unit. Nucleic Acids Res 8:5993–6005
Harris DJ, Crandall KA (2000) Intragenomic variation within ITS1 and ITS2 of freshwater crayfishes (Decapoda: Cambaridae): implications for phylogenetic and microsatellite studies. Mol Biol Evol 17:284–291
Hsueh JYC, Bohm RP Jr, Didier PJ, Tang X, Lasbury ME, Li B, Bartlett MS, Smith JW, Lee CH (2001) Internal transcribed spacer regions of rRNA genes of Pneumocystis carinii from monkeys. Clin Diag Lab Immunol 8:503–508
Kochzius M, Nölte M, Weber H, Silkenbeumer N, Hjörleifsdottir S, Hreggvidsson GO, Marteinsson V, Kappel K, Planes S, Tinti F, Magoulas A, Garcia Vazquez E, Turan C, Hervet C, Campo Falgueras D, Antoniou A, Landi M, Blohm D (2008) DNA microarrays for identifying fishes. Mar Biotechnol 10:207–217
Subrahmanyam CS, Cassidy B, Busch H, Rothblum LI (1982) Nucleotide sequence of the region between the 18S rRNA sequence and the 28S rRNA sequence of rat ribosomal DNA. Nucleic Acids Res 10:3667–3680
Sumida M, Kato Y, Kurabayashi A (2004) Sequencing and analysis of the internal transcribed spacers (ITSs) and coding regions in the EcoRI fragment of the ribosomal DNA of the Japanese pond frog Rana nigromaculata. Genes Genet Syst 79:105–118
von der Schulenburg JHG, English U, Wägele JW (1999) Evolution of ITS1 rDNA in the Digenea (Platyhelminthes: Trematoda): 39 end sequence conservation and its phylogenetic utility. J Mol Evol 48:2–12
von der Schulenburg JHG, Hancock JM, Pagnamenta A, Sloggett JJ, Majerus MEN, Hurst GDD (2001) Extreme length and length variation in the first ribosomal internal transcribed spacer of ladybird beetles (Coleoptera: Coccinellidae). Mol Biol Evol 18:648–660
Acknowledgements
We would like to thank M. Hamaguchi, National Research Institute of Fisheries and Environment of Inland Sea; T. Yanagimoto, National Research Institute of Far Seas Fisheries; and T. Yoshimura, Seikai National Fisheries Research Institute for sharing their invaluable specimens. We also thank S. Katayama, S. Kawashima, and H. Kurogi, National Research Institute of Fisheries Science for assisting in sample collection in the Arasaki area and M. Michibayashi and H. Hasegawa for their technical assistance with the DNA analysis. This work was supported by a Grant-in-Aid for Scientific Research on Priority Areas (B) (No. 17380126) from the Ministry of Education, Science, Sports, and Culture, Japan.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Chow, S., Ueno, Y., Toyokawa, M. et al. Preliminary Analysis of Length and GC Content Variation in the Ribosomal First Internal Transcribed Spacer (ITS1) of Marine Animals. Mar Biotechnol 11, 301–306 (2009). https://doi.org/10.1007/s10126-008-9153-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10126-008-9153-2