Vertebrate genome evolution and the zebrafish gene map.

In chordate phylogeny, changes in the nervous system, jaws, and appendages transformed meek filter feeders into fearsome predators. Gene duplication is thought to promote such innovation. Vertebrate ancestors probably had single copies of genes now found in multiple copies in vertebrates and gene maps suggest that this occurred by polyploidization. It has been suggested that one genome duplication event occurred before, and one after the divergence of ray-finned and lobe-finned fishes. Holland et al., however, have argued that because various vertebrates have several HOX clusters, two rounds of duplication occurred before the origin of jawed fishes. Such gene-number data, however, do not distinguish between tandem duplications and polyploidization events, nor whether independent duplications occurred in different lineages. To investigate these matters, we mapped 144 zebrafish genes and compared the resulting map with mammalian maps. Comparison revealed large conserved chromosome segments. Because duplicated chromosome segments in zebrafish often correspond with specific chromosome segments in mammals, it is likely that two polyploidization events occurred prior to the divergence of fish and mammal lineages. This zebrafish gene map will facilitate molecular identification of mutated zebrafish genes, which can suggest functions for human genes known only by sequence.

zALK-8, a novel type I serine/threonine kinase receptor, is expressed throughout early zebrafish development.

Here, we report the isolation and characterization of zebrafish activin receptor-like kinase-8 (zALK-8), a novel type I serine/threonine (ser/thr) kinase receptor of the transforming growth factor beta (TGF-beta) family. zALK-8 is novel, in that it contains an extracellular domain that is quite distinct from that of previously identified ALK receptors 1 through 7. Analysis of the predicted amino acid sequence of the 506 amino acid zALK-8 receptor reveals an ser/thr kinase domain characteristic of type I TGF-beta family member receptors. zALK-8, therefore, is a traditional type I ser/thr kinase receptor of the TGF-beta family, but it may exhibit novel ligand-binding activities. The developmental expression of zALK-8 mRNA was examined by wholemount in situ hybridization analysis using a probe from the 3'-untranslated sequence of zALK-8, which does not cross react with other members of the highly conserved TGF-beta receptor family. zALK-8 mRNA is present as a maternal message that is expressed ubiquitously before the start of zygotic transcription. By 16 hr postfertilization (hpf), zALK-8 mRNA is still expressed fairly evenly throughout the embryo. In 24-hpf embryos, zALK-8 mRNA is expressed predominantly in the developing eye and neural structures. By 48 hpf, zALK-8 mRNA is faintly detectable as a diffuse signal throughout the head. zALK-8 mRNA is not detectable by this method in 72-hpf or 96-hpf embryos. Northern analysis of zALK-8 mRNA in poly(A+) mRNA isolated from 6-9 hpf embryos detects a major transcript of 3.6 kb and a minor transcript of 4.3 kb. zALK-8 mRNA expression correlates well with known functions of TGF-beta family members as early axial patterning and mesoderm-inducing growth factors and as potent growth and differentiation factors in craniofacial development.