Sequence comparison of the ribosomal DNA internal transcribed spacers (ITSs) and 5.8S ribosomal gene and their secondary structures in 17 Pteriomorphian bivalves

Abstract

Purpose and Approach: The first and second internal transcribed spacer (ITS1 and ITS2) region of the ribosomal DNA and 5.8S rRNA gene from 17 pteriomorphian bivalve species Amusium pleuronectes, Mimichlamys nobilis, Mimichlamys seneatoria, Mimichlamys sp.NT-2006, Minnivolva pyxidatus, Semipallium fulvicostat, Decatopecten radula (Family-Pectinidae), Perna calaiculus, Perna perna, Perna picta and Aulacomy atra maorian (Family-Mytilinae) and Crassostrea ariakensis, Dendostrea crenulifera, Ostrea circumpicta, Hyotissa hyotis and Spondylus varius (Family-Ostreidae)and Saccostrea kegak (FamilySpondylidae) were analyzed.Results: The size of ITS1 sequence ranged from 21bp to 475bp with GC contents ranged from 25.84% to 50.00 %. The size of ITS2 ranged from 233bp to 504bp with GC contents from 28.91% to 51.69%. The size of 5.8S ranged from 127bp to 167bp with GC contents ranged from 32.73% to 46.67% depending on species. Extensive sequence variation and obvious polymorphism were noted for ITS1, ITS2 regions in these species, and ITS2 similarity was higher than that of ITS1 across the species. The size of 5.8S rRNA gene sequence length was specific to family. The phylogenetic tree was constructed by Neighbor-joining method and maximum –parsimony method. The topology indicates that pectinidae was closely related to myitilinae than the ostreidae and spondylidae to Ostreidae. The secondary structure analysis of ITS1, ITS2 and 5.8S indicated a phylogentic relationship among the selected species belonging to different geographical locations.Conclusions: Several common features of secondary structure are shared among these species, with some of them supported by compensative changes suggesting the significant role by ITS2 as an RNA domain during ribosomal biogenesis.