Type of the lecture:
Workshop
Organizers:
Mutsumi NISHIDA (Tokyo Univ.)
Program:
Actinopterygii, the ray-finned fish, is the most diversified group of all vertebrates, currently comprising over 25,000 species placed in 42 orders, 431 families, and 4075 genera. Because of the enormous species diversity involved, ancient origin that goes back some 400 million years ago, and the wide ranging variations not only in morphology but also in behavior, ecology, and physiology, there remains much controversy over the higher-level relationships of actinopterygians. Our research group has determined complete mitochondrial DNA sequences from unprecedentedly large number of species (ca. 500) that covers a whole spectrum of actinopterygian diversity. We will present results from phylogenetic analyses of this large data set which is divided into the following three hierarchical levels: 1) basal actinopterygians; 2) higher actinopterygians; and 3) percomorphs. We have discovered many examples of previously-unrecognized, major comprehensive groups of actinopterygians with high statistical support through preliminary phylogenetic analysis.
Hox genes play a key role in determination of axial and appendicular skeletal morphology and may be a key component of the evolution of diverse metazoan body forms. It has been widely assumed that differences in their organization and deployment are thought to play a important role in producing variant body patterns in all vertebrate evolution. While mammals have four clusters composed of 39 Hox genes, the number of Hox genes and clusters is diversified in among teleost fish. To test the possibility that Hox organization may have varied since the origin of jawed vertebrates, we have studied the Hox gene clusters in medaka fish. We isolated BAC clones that cover the entire Hox gene loci, and characterized them by shot-gun sequencing. Although it has not been completed, at least 46 Hox genes are encoded in seven clusters in medaka. Our data show that gene organization of the medaka clusters is quite similar to that of Fugu clusters, but there is a little difference from zebrafish clusters, and an unprecedented degree of variation when compared with the present mammalian clusters.
The Japanese pufferfish, Fugu rubripes, is a specialized teleost belonging to the order Tetraodontiformes and family Tetraodontidae. It is unique among vertebrates in that it has the smallest vertebrate genome yet characterized. Its haploid genome size is only 365 Mb, about one-eighth the size of the human genome and one-quarter the size of the zebrafish genome. Thus, it constitutes an interesting model for understanding the evolution and divergence of vertebrates. A 'draft' sequence of the Fugu genome was determined by the 'whole-genome shotgun' sequencing strategy and annotated using automated annotation pipeline. About 30,000 genes have been predicted in the Fugu genome, similar to that in the human genome. As previously predicted, Fugu genome contains less than 15% repetitive sequences, which largely accounts for the compact genome size. Comparisons of the Fugu and the human genome sequences have identified several novel genes in the human genome, a set of about 8000 genes in the human genome that are either quite divergent or absent in Fugu (and presumably in other fishes), conserved syntenic regions and duplicated genes. Since the conserved syntenic regions share a common evolutionary history, they should be useful for understanding the evolutionary changes in the fish and mammalian lineages.
Medaka (Oryzias latipes) is emerging as an important model fish that is phylogenically distant from zebrafish but closer to pufferfish. With the recent additions of the genetic toolkits such as BAC recourses and WGS sequences, the highly dense genome markers based on polymorphic inbred strains, which is essential for genome assembly with high quality also come to be available. About 1600 markers including 1000 randomly selected EST markers were mapped, and all of them are successfully grouped into 24 linkage groups that correspond to medaka chromosome number. This genomic map is a powerful tool for positional cloning of mutated genes in medaka, and the syntenies of medaka, pufferfish and zebrafish genes to human genome provide evidence of the whole genome duplication occurred after divergence of fish and tetrapods and before divergence of medaka and zebrafish. For a gene regulation study, polyploidy in model fish species might be advantageous, since regulatory elements and functional domains in each of the fish duplicates may have unique roles in their function. And medaka and zebrafish may have considerably different sets of genes with subfunctional or neofunction because this degeneration process would have affected different genes in the two fish lineage.