**1. Introduction**

Contrary to their synthetic counterparts, the demand for natural pigments has been steadily increasing in recent years in response to global market shifts and consumer preferences [1,2]. Filamentous fungi have been gaining recognition as a potential microbial source of natural pigments; however, the industrial applications of these microorganisms are not as widespread as those involving algae or bacteria [3]. Fungi can potentially produce a wide range of pigments, such as carotenoids, *Monascus* pigments, and melanins [4–8], and can utilize a wide range of substrates, thus making the medium composition design and fermentation process more flexible [9].

However, fungal pigments are secondary metabolites, and most of their synthesis pathways and optimal production conditions remain largely unknown [10], which limits their optimization and widespread adoption in industrial applications. Fortunately, with

**Citation:** Oh, J.-J.; Kim, Y.J.; Kim, J.Y.; Kwon, S.L.; Lee, C.; Lee, M.-E.; Kim, J.W.; Kim, G.-H. Genomic Analysis and Assessment of Melanin Synthesis in *Amorphotheca resinae* KUC3009. *J. Fungi* **2021**, *7*, 289. https://doi.org/ 10.3390/jof7040289

Academic Editor: Laurent Dufossé

Received: 22 March 2021 Accepted: 9 April 2021 Published: 12 April 2021

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the accumulation of high-throughput sequencing data, bioinformatics tools can be used to identify putative genes or gene clusters involved in metabolite production. Afterward, comprehensive prediction of the provisional biosynthetic pathways of pigments would be possible based on the identified putative genes or gene clusters [11]. Therefore, genomic studies could provide fundamental insights into the pathways associated with secondary metabolite synthesis in fungi, thus paving the way for their adoption in industrial-scale processes. We previously reported the promising capacity of the fungus *Amorphotheca resinae* KUC3009 to produce melanin at an industrial scale due to its antioxidant activity and high metal ion adsorption capability [8,12]. However, general information on the mechanisms of melanin or melanin-related pigment biosynthesis in *A*. *resinae* is not yet available. Therefore, understanding the mechanisms involved in melanin biosynthesis using bioinformatic tools would provide critical insights to optimize scalable pigment production using fungi.

Our study sequenced and assembled the whole genome of *A*. *resinae* KUC3009. After gene annotation, the putative genes and gene clusters involved in pigment formation were comprehensively investigated. Afterward, the involvement of putative genes or gene clusters was further corroborated with biochemical and molecular approaches. Based on these results, we proposed potential strategies for the optimization of scalable melanin production. Therefore, our study establishes a robust foundation for the production of secondary metabolites using *A*. *resinae*, as well as fundamental guidelines for future studies to improve upon.
