Preliminary Analysis of Length and GC Content Variation in the Ribosomal First Internal Transcribed Spacer (ITS1) of Marine Animals
- 270 Downloads
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.
KeywordsGC content ITS1 Length Marine animals Phylogenetic utility
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.
- 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 10:207–217PubMedCrossRefGoogle Scholar