Phenylalanine Ammonia-Lyase: A Key Gene for Color Discrimination of Edible Mushroom Flammulina velutipes

• Published in: Journal of fungi (Basel) Vol. 9; no. 3; p. 339
• Main Authors: Im, Ji-Hoon, Yu, Hye-Won, Park, Che-Hwon, Kim, Jin-Woo, Shin, Ju-Hyeon, Jang, Kab-Yeul, Park, Young-Jin
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 09-03-2023; MDPI
• Subjects: Agricultural biotechnology; Biosynthesis; Color; Cultivars; Flammulina velutipes; Fruit bodies; fruiting body color; Gene deletion; Genes; genome; Genomes; Humidity; Mushrooms; Mutation; Open reading frames; Phenylalanine; Phenylalanine ammonia-lyase; Polymerase chain reaction; Single-nucleotide polymorphism; Threonine; Variation; United States > US; Japan; genome; fruiting body color; phenylalanine ammonia-lyase; Flammulina velutipes
• ISSN: 2309-608X; 2309-608X
• DOI: 10.3390/jof9030339

In nature;
, also known as winter mushrooms, vary in the color of their fruiting bodies, from black, yellow, pale yellow, or beige to white. The purpose of this study was to compare the genome sequences of different colored strains of
and to identify variations in the genes associated with fruiting body color. Comparative genomics of six
strains revealed 70 white-strain-specific variations, including single nucleotide polymorphisms (SNPs) and insertions/deletions (indels), in the genome sequences. Among them, 36 variations were located in the open reading frames, and only one variation was identified as a mutation with a disruptive in-frame deletion (ΔGCGCAC) within the annotated gene phenylalanine ammonia-lyase 1 (
). This mutation was found to cause a deletion, without a frameshift, of two amino acids at positions 112 and 113 (arginine and threonine, respectively) in the
gene of the white strain. Specific primers to detect this mutation were designed, and amplification refractory mutation system (ARMS) polymerase chain reaction (PCR) was performed to evaluate whether the mutation is color specific for the
fruiting body. PCR analysis of a total of 95
strains revealed that this mutation was present only in white strains. In addition, monospores of the heterozygous mutant were isolated, and whether this mutation was related to the color of the fruiting body was evaluated by a mating assay. In the mating analysis of monospores with mutations in
, it was found that this mutation plays an important role in determining the color of the fruiting body. Furthermore, the deletion (Δ
RT
) in
is located between motifs that play a key role in the catalytic function of FvPAL1. These results suggest that this mutation can be used as an effective marker for the color-specific breeding of
, a representative edible mushroom.