PUBLICATION
Conserved synteny and the zebrafish genome
- Authors
- Catchen, J.M., Braasch, I., and Postlethwait, J.H.
- ID
- ZDB-PUB-110921-17
- Date
- 2011
- Source
- Methods in cell biology 104: 259-285 (Chapter)
- Registered Authors
- Braasch, Ingo, Postlethwait, John H.
- Keywords
- conserved synteny, genome duplication, NGF, nerve growth factor receptor, ohnolog, teleost
- MeSH Terms
-
- Animals
- Data Mining/methods
- Databases, Genetic
- Evolution, Molecular
- Fish Proteins/genetics
- Gene Deletion
- Gene Duplication
- Genome*
- Humans
- Models, Genetic
- Phylogeny
- Receptors, Nerve Growth Factor/genetics
- Sequence Homology, Nucleic Acid
- Smegmamorpha/genetics
- Synteny*
- Zebrafish/genetics*
- PubMed
- 21924168 Full text @ Meth. Cell. Biol.
Citation
Catchen, J.M., Braasch, I., and Postlethwait, J.H. (2011) Conserved synteny and the zebrafish genome. Methods in cell biology. 104:259-285.
Abstract
Zebrafish offers significant opportunities for the investigation of vertebrate development, evolution, physiology, and behavior and provides numerous models of human disease. Connecting zebrafish phenogenetic biology to that of humans and other vertebrates, however, requires the proper assignment of gene orthologies. Orthology assignments by phylogenetic analysis or by reciprocal best sequence similarity searches can lead to errors, especially in cases of gene duplication followed by gene loss or rapid lineage-specific gene evolution. Conserved synteny analysis provides a method that helps overcome such problems. Here we describe conserved synteny analysis for zebrafish genes and discuss the Synteny Database, a website specifically designed to identify conserved syntenies for zebrafish that takes into account the teleost genome duplication (TGD). We utilize the Synteny Database to demonstrate its power to resolve our understanding of the evolution of nerve growth factor receptor related genes, including Ngfr and the enigmatic Nradd. Finally, we compare conserved syntenies between zebrafish, stickleback, spotted gar, and human to understand the timing of chromosome rearrangements in teleost genome evolution. An improved understanding of gene histories that comes from the application of tools provided by the Synteny Database can facilitate the connectivity of zebrafish and human genomes.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping