title: Bioinformatic Characterization of Genes and Proteins Involved in Blood Clotting in Lampreys.
abstract: Lampreys and hagfish are the earliest diverging of extant vertebrates and are obvious targets for investigating the origins of complex biochemical systems found in mammals. Currently, the simplest approach for such inquiries is to search for the presence of relevant genes in whole genome sequence (WGS) assemblies. Unhappily, in the past a high-quality complete genome sequence has not been available for either lampreys or hagfish, precluding the possibility of proving gene absence. Recently, improved but still incomplete genome assemblies for two species of lamprey have been posted, and, taken together with an extensive collection of short sequences in the NCBI trace archive, they have made it possible to make reliable counts for specific gene families. Particularly, a multi-source tactic has been used to study the lamprey blood clotting system with regard to the presence and absence of genes known to occur in higher vertebrates. As was suggested in earlier studies, lampreys lack genes for coagulation factors VIII and IX, both of which are critical for the "intrinsic" clotting system and responsible for hemophilia in humans. On the other hand, they have three each of genes for factors VII and X, participants in the "extrinsic" clotting system. The strategy of using raw trace sequence "reads" together with partial WGS assemblies for lampreys can be used in studies on the early evolution of other biochemical systems in vertebrates.
authors.affiliation: Departments of Chemistry & Biochemistry and Molecular Biology, University of California, San Diego, La Jolla, CA, 92093-0314, USA. rdoolittle@ucsd.edu.
authors.forename: Russell F
authors.initials: RF
authors.lastname: Doolittle
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D001777:Blood Coagulation / Q000235:genetics*; D002570:Ceruloplasmin / Q000378:metabolism; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D055106:Genome-Wide Association Study / Q000662:veterinary; D006196:Hagfishes / Q000235:genetics; D007798:Lampreys / Q000097:blood* / Q000235:genetics*; D010802:Phylogeny; D014812:Vitamin K / Q000097:blood
chemical_list: D014812:Vitamin K; D002570:Ceruloplasmin
keywords: Blood clotting; Lampreys; Trace databases; Whole genome sequence assembly problems