(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) > cellular organisms: NE > Eukaryota: NE > Opisthokonta: NE > Metazoa: NE > Eumetazoa: NE > Bilateria: NE > Deuterostomia: NE > Chordata: NE > Craniata: NE > Vertebrata: NE > Gnathostomata: NE > Teleostomi: NE > Euteleostomi: NE > Actinopterygii: NE > Actinopteri: NE > Neopterygii: NE > Teleostei: NE > Osteoglossocephalai: NE > Clupeocephala: NE > Euteleosteomorpha: NE > Neoteleostei: NE > Eurypterygia: NE > Ctenosquamata: NE > Acanthomorphata: NE > Euacanthomorphacea: NE > Percomorphaceae: NE > Eupercaria: NE > Tetraodontiformes: NE > Tetraodontoidei: NE > Tetradontoidea: NE > Tetraodontidae: NE > Takifugu: NE > Takifugu rubripes: NE
LegendThis sequence has been compared to family alignement (MSA) red => minority aminoacid blue => majority aminoacid color intensity => conservation rate title => sequence position(MSA position)aminoacid rate Catalytic site Catalytic site in the MSA MVTLCHYAIIVLLPHFLSVSSADENDLLVTVKNGKVQGTLLPVLNGNVRA FLGIPYAKPPVGKLRFRNPEPIDSWEGVKNANSFSNTCFQLADMTFAGFR GAEMWNPNTPVNEDCLYLNVWTPQAQASSPLPVMIWIYGGGFTTGTSSLE LYDGRYLTKSEDVIVVSMNYRVGVLGFLSLPNNTNVHGNAGLMDQRLAIQ WVVDNIAAFGGDPSQITLFGESAGSVCVGFHVLSPGSNVLFKRAVMQSGA PTAHWTTVSLSEAWNRSTMLGMSVGCNKPIELETCLQSINVSHLVTVQYG VLSNPSTSDIPFLPVVDGDFLPDEVDALISNSSIQKKEVFLGLNHDEGTY FLVYTVAGFDITSQSLITKAQFLNGLDHILASAQTITKETVTFQYTDWAD EENGTKNRDSLNRMLSEYMFICPVTDFAYRYQKAGGKPFLYYFQHRSSRN PWPEWMGVMHGYEIEFVFGLPLNPSLGYTEEEVNMSKRFMKYWATFARTG FVWNPGIDGQPWPMFTSEKREYVTLDTQNPEYKSNLRADDCQFWNSLIPQ IRKMAADLQTCSGAIEPILSFTSFLLMSLYYLLIQ
Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published, analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination and developmental genetics. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approximately 2,900 new genes, using 5'-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of approximately 50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.
The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.
