Intergenic Spacer Of Ribosomal DNA In Setaria And Their Phylogenetic Implications

The genus Setaria belongs to Gramineae. In this genus,there are bout 125 species which widely distributed in the world including many weed species and Setaria italica, an ancient cereal crop. So far three genome types were identified in the genus, A genome, B genome and C genome. But the genome composition of most species is unknown and both of phylogenetic and genomic relationships in Setaria are still poorly understood. IGS sequences from some Setaria genus were cloned and sequenced so as to characterize their subrepeat types and C repeat structures. Those sequences were also used to analyze phylogenetic relaships among different genomes of Setaria and among different species. The major results were as follows:1. We had analyzed the sequences of IGS from the samples used, and found that each genome has its own type of subrepeat. Although the species are different, the types of subrepeat are consistent, especially in A genome. From difference of subrepeat types we deduce that S.lac-W74 has a new genome in Setaria which we named D. The subrepeat type from Setaria pumila and its close relatives showed clear different from that of the known A/B/C genomes, indicating that its genome is also a novel one which we named as E genome.2. We had conducted a study of C repeat, and found that there are two C repeats, C I and CⅡ, in the sequence of IGS. The CⅠare consistent in a certain genome, but they have polymorphism among different genomes. CⅡis much more polymorphism among different accessions of the same sepecies, which could provides information to further reserch of taxonomy. Though the analysis of C repeat, we found S.lac-W74 and Setaria pumila (L.)Beauv have different C repeat from other genomes, which support the idea that both of them belongs to new genomes.3. An IGS sequence from Panicum miliaceum (GenBank accession number:AF147502) was used to construct phylogenetic trees. We ran ML and NJ analysis in PAUP*4.0 and PHYLIP3.69,and NJ analysis in MEGA4.1 (beta), too.The phylogenetic trees were draw by Treeview. We got similar result from those different analyses. The result indicated that the genome of Setaria pumila (L.)Beauv separates from other genomes of Setaria. One genome of S.lac-W74 (4X) showed some way close phylogenetic relation with A,B,C genomes, although it located in different small branch of the tree. Cluster analysis supports that genomes from S.lac-W74 and Setaria pumila (L.)Beauv belonging to new genomes, which confirm the inference of Setaria pumila (L.)Beauv and Setaria viridis (L.) Beauv having different origins.