PUBLICATION

Phenoscape: Identifying candidate genes for evolutionary phenotypes

Authors
Edmunds, R.C., Su, B., Balhoff, J.P., Eames, B.F., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M.
ID
ZDB-PUB-151027-7
Date
2016
Source
Molecular Biology and Evolution   33(1): 13-24 (Journal)
Registered Authors
Edmunds, Richard, Mabee, Paula M., Westerfield, Monte
Keywords
molecular evolution, gene expression, evolutionary phenotypes, catfish, nonmodel organism
MeSH Terms
  • Animals
  • Catfishes/genetics*
  • Computational Biology
  • Evolution, Molecular*
  • Gene Expression*/genetics
  • Gene Expression*/physiology
  • Models, Genetic*
  • Phenotype*
  • Software
PubMed
26500251 Full text @ Mol Bio Evol
Abstract
Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in non-model organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved via disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology.
Genes / Markers
Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes