Phenoscape: identifying candidate genes for evolutionary phenotypes

Edmunds, Richard C., Su, Baofeng, Balhoff, James P., Eames, B. Frank, Dahdul, Wasila M., Lapp, Hilmar, Lundberg, John G., Vision, Todd J., Dunham, Rex A., Mabee, Paula M., and Westerfield, Monte (2015) Phenoscape: identifying candidate genes for evolutionary phenotypes. Molecular Biology and Evolution, 33 (1). pp. 13-24.

[img]
Preview
PDF (Published Version) - Published Version
Available under License Creative Commons Attribution.

Download (1MB) | Preview
View at Publisher Website: http://dx.doi.org/10.1093/molbev/msv223
 
38


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 nonmodel 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 tomutant 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 through 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.

Item ID: 51379
Item Type: Article (Research - C1)
ISSN: 1537-1719
Keywords: molecular evolution, gene expression, evolutionary phenotypes, catfish, nonmodel organism
Additional Information:

The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Funders: National Science Foundation (NSF), National Evolutionary Synthesis Center, National Institutes of Health (NIH)
Projects and Grants: NSF DBI-0641025, NSF DBI-1062404, NSF DBI-1062542, NSF EF-0423641, NSF EF-0905606, NIH HG002659, NIH HD22486
Date Deposited: 02 Nov 2017 01:58
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060403 Developmental Genetics (incl Sex Determination) @ 50%
06 BIOLOGICAL SCIENCES > 0604 Genetics > 060409 Molecular Evolution @ 50%
SEO Codes: 96 ENVIRONMENT > 9601 Air Quality > 960106 Urban and Industrial Air Quality @ 100%
Downloads: Total: 38
Last 12 Months: 13
More Statistics

Actions (Repository Staff Only)

Item Control Page Item Control Page