THE INTERNAL TRANSCRIBED SPACER-2 EXHIBITS A COMMON SECONDARY STRUCTURE IN GREEN-ALGAE AND FLOWERING PLANTS

Sequences of the Internal Transcribed Spacer 2 (ITS-2) regions of the nuclear rDNA repeats from 111 organisms of the family Volvocaceae (Chl orophyta) and unicellular organisms of the Volvocales, including Chlam ydomonas reinhardtii, were determined. The use of thermodynamic energy optimization to generate secondary structures and phylogenetic compar ative analysis of the spacer regions revealed a common secondary struc ture that is conserved despite wide intra- and interfamilial primary s equence divergence. The existence of this conserved higher-order struc ture is supported by the presence of numerous compensating basepair ch anges as well as by an evolutionary history of insertions and deletion s that nevertheless maintains major aspects of the overall structure. Furthermore, this general structure is preserved across broad phylogen etic lines, as it is observed in the ITS-2s of other chlorophytes, inc luding flowering plants; previous reports of common ITS-2 secondary st ructures in other eukaryotes were restricted to the order level. The r eported ITS-2 structure possesses important conserved structural motif s which may help to mediate cleavages in the ITS-2 that occur during r RNA transcript processing. Their recognition can guide further studies of eukaryotic rRNA processing, and their application to sequence alig nments may contribute significantly to the value of ITS-2 sequences in phylogenetic analyses at several taxonomic levels, but particularly i n characterizing populations and species.