title: Genomic evidence for a simpler clotting scheme in jawless vertebrates.
abstract: Mammalian blood clotting involves numerous components, most of which are the result of gene duplications that occurred early in vertebrate evolution and after the divergence of protochordates. As such, the genomes of the jawless fish (hagfish and lamprey) offer the best possibility for finding systems that might have a reduced set of the many clotting factors observed in higher vertebrates. The most straightforward way of inventorying these factors may be through whole genome sequencing. In this regard, the NCBI Trace database ( http://www.ncbi.nlm.nih.gov/Traces/trace.cgi ) for the lamprey (Petromyzon marinus) contains more than 18 million raw DNA sequences determined by whole-genome shotgun methodology. The data are estimated to be about sixfold redundant, indicating that coverage is sufficiently complete to permit judgments about the presence or absence of particular genes. A search for 20 proteins whose sequences were determined prior to the trace database study found all 20. A subsequent search for specified coagulation factors revealed a lamprey system with a smaller number of components than is found in other vertebrates in that factors V and VIII seem to be represented by a single gene, and factor IX, which is ordinarily a cofactor of factor VIII, is not present. Fortuitously, after the completion of the survey of the Trace database, a draft assembly based on the same database was posted. The draft assembly allowed many of the identified Trace fragments to be linked into longer sequences that fully support the conclusion that lampreys have a simpler clotting scheme compared with other vertebrates. The data are also consistent with the hypothesis that a whole-genome duplication or other large scale block duplication occurred after the divergence of jawless fish from other vertebrates and allowed the simultaneous appearance of a second set of two functionally paired proteins in the vertebrate clotting scheme.
authors.affiliation: Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0314, USA. rdoolittle@ucsd.edu
authors.forename: Russell F
authors.initials: RF
authors.lastname: Doolittle
authors.forename: Yong
authors.initials: Y
authors.lastname: Jiang
authors.forename: Justin
authors.initials: J
authors.lastname: Nand
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001779:Blood Coagulation Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D020451:Contig Mapping; D030541:Databases, Genetic; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics; D005165:Factor V / Q000737:chemistry; D005169:Factor VIII / Q000737:chemistry; D016678:Genome / Q000235:genetics; D023281:Genomics; D006801:Humans; D008969:Molecular Sequence Data; D010447:Peptide Hydrolases / Q000235:genetics / Q000378:metabolism; D048428:Petromyzon / Q000235:genetics*; D010802:Phylogeny; D016415:Sequence Alignment; D014812:Vitamin K / Q000378:metabolism
chemical_list: D001779:Blood Coagulation Factors; D014812:Vitamin K; D005165:Factor V; D005169:Factor VIII; D010447:Peptide Hydrolases