Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidis

Authors

Wheaton L. Schroeder, University of Nebraska - LincolnFollow
Rajib Saha, National University of SingaporeFollow

Date of this Version

2020

Document Type

Article

Citation

Schroeder and Saha, Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidis, STAR Protocols (2020), https://doi.org/10.1016/j.xpro.2020.100105

Comments

2020 The Author(s).

Abstract

Exophiala dermatitidis is a polyextremotolerant fungus with a small genome, thus suitable as a model system for melanogenesis and carotenogensis. A genome-scale model, iEde2091, is reconstructed to increase metabolic understanding and used in a shadow price analysis of pigments, as detailed here. Important to this reconstruction is OptFill, a recently developed alternative gap-filling method useful in the holistic and conservative reconstruction of genome-scale models of metabolism, particularly for understudied organisms like E. dermatitidis where gaps in metabolic knowledge are abundant. For complete details on the use and execution of this protocol, please refer to Schroeder and Saha (2020) and Schroeder et al. (2020).