Submitted:
10 October 2025
Posted:
13 October 2025
You are already at the latest version
Abstract
Keywords:
1. Introduction
2. Materials and Methods
2.1. Fungal Strain
2.2. Medium and Strain Culture
2.3. Monascus Pigments Production Under Salt Stress
2.4. Analysis of Monascus flavor with GC-IMS
2.5. Transcriptome Sequencing Analysis
2.6. Statistical Analysis
3. Results and Discussion
3.1. Effect of NaCl on the Growth in M. ruber CICC41233
3.2. Effect of NaCl on Monascus Pigment Production
3.3. Effect of NaCl on Monascus Flavor Fingerprint
3.4. Transcriptomic Insights into the Metabolic Regulation of M. ruber Cultivated on Solid Substrate
3.5. Transcriptomic Insights into the Monascus Pigment Fermentation and Monascus flavor of M. ruber
3.6. Monascus Pigment Biosynthetic Gene Cluster Expression Under Salt Condition in M. ruber CICC41233
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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| Sample* | Alcohol | Aldehyde | Ketone | Ester | Acid | Pyrazine | Others |
| CK-Y3 | 21.30% | 33.34% | 41.63% | 1.92% | 0.36% | 0.09% | 1.35% |
| TY1-3 | 18.78% | 33.73% | 43.64% | 1.90% | 0.29% | 0.08% | 1.59% |
| TY3-3 | 25.71% | 17.73% | 51.28% | 3.36% | 0.32% | 0.12% | 1.47% |
| TY5-3 | 15.96% | 29.80% | 50.07% | 2.93% | 0.26% | 0.10% | 0.87% |
| CK-Y6 | 16.59% | 26.63% | 52.87% | 2.15% | 0.38% | 0.10% | 1.28% |
| TY1-6 | 11.38% | 44.00% | 42.22% | 1.32% | 0.27% | 0.09% | 0.71% |
| TY3-6 | 18.64% | 36.44% | 42.10% | 1.66% | 0.33% | 0.08% | 0.74% |
| TY5-6 | 20.84% | 31.17% | 45.18% | 1.68% | 0.20% | 0.11% | 0.82% |
| DEG Set* | DEG Number | Up-regulated | Down-regulated |
| CK-G3 vs TG1-3 | 199 | 99 | 100 |
| CK-G3 vs TG5-3 | 1351 | 336 | 1015 |
| CK-G6 vs TG1-6 | 356 | 172 | 184 |
| CK-G6 vs TG5-6 | 1319 | 315 | 1004 |
| CK-G3 vs CK-G6 | 623 | 523 | 100 |
| TG1-3 vs TG1-6 | 633 | 522 | 111 |
| TG5-3 vs TG5-6 | 696 | 581 | 115 |
| CK-Y3 vs TY1-3 | 1078 | 662 | 416 |
| CK-Y3 vs TY5-3 | 2873 | 1749 | 1124 |
| CK-Y6 vs TY1-6 | 3681 | 3264 | 417 |
| CK-Y6 vs TY5-6 | 3530 | 2426 | 1104 |
| CK-Y3 vs CK-Y6 | 2755 | 1510 | 1245 |
| TY1-3 vs TY1-6 | 4451 | 3340 | 1111 |
| TY5-3 vs TY5-6 | 2757 | 1784 | 973 |
| DEG Set | Pathway ID | KEGG Pathway | Number of Genes | p-value |
qvalue |
| CK-G3 vs TG1-3 | ko00785 | Lipoic acid metabolism | 1 | 0.020172 | 0.259847 |
| ko00564 | Glycerophospholipid metabolism | 2 | 0.046493 | 0.259847 | |
| CK-G3 vs TG5-3 | ko00380 | Tryptophan metabolism | 14 | 0.000009 |
0.000321 |
| ko00360 | Phenylalanine metabolism | 12 | 0.000011 | 0.000321 | |
| ko00620 | Pyruvate metabolism | 12 | 0.000088 | 0.001917 | |
| ko00350 | Tyrosine metabolism | 9 | 0.001026 | 0.017855 | |
| ko00500 | Starch and sucrose metabolism | 10 | 0.003144 | 0.045581 | |
| CK-G6 vs TG1-6 | ko00564 | Glycerophospholipid metabolism | 5 | 0.005180 | 0.126913 |
| ko00592 | alpha-Linolenic acid metabolism | 2 | 0.015765 | 0.229069 | |
| ko00052 | Galactose metabolism | 3 | 0.018699 | 0.229069 | |
| ko00591 | Linoleic acid metabolism | 1 | 0.043982 | 0.359187 | |
| CK-G6 vs TG5-6 | ko00360 | Phenylalanine metabolism | 10 | 0.000878 | 0.039661 |
| ko00520 | Amino sugar and nucleotide sugar metabolism | 12 | 0.001293 | 0.039661 | |
| ko00380 | Tryptophan metabolism | 11 | 0.002274 | 0.043861 | |
| ko00350 | Tyrosine metabolism | 9 | 0.002384 | 0.043861 | |
| CK-G3 vs CK-G6 | ko00520 | Amino sugar and nucleotide sugar metabolism | 8 | 0.000287 | 0.008184 |
| ko00500 | Starch and sucrose metabolism | 7 | 0.001016 | 0.019304 | |
| ko01212 | Fatty acid metabolism | 5 | 0.004113 | 0.046890 | |
| TG1-3 vs TG1-6 | ko00590 | Arachidonic acid metabolism | 3 | 0.000233 | 0.005547 |
| ko00592 | alpha-Linolenic acid metabolism | 4 | 0.000248 | 0.005547 | |
| ko00591 | Linoleic acid metabolism | 2 | 0.001552 | 0.023848 | |
| ko00561 | Glycerolipid metabolism | 6 | 0.001780 | 0.023848 | |
| ko00430 | Taurine and hypotaurine metabolism | 3 | 0.002910 | 0.031995 | |
| ko00500 | Starch and sucrose metabolism | 7 | 0.003343 | 0.031995 | |
| TG5-3 vs TG5-6 | ko00130 | Ubiquinone and other terpenoid-quinone biosynthesis | 5 | 0.000428 | 0.014330 |
| DEG Set | Pathway ID | KEGG Pathway | Number of Genes | p-value |
qvalue |
| CK-Y3 vs TY1-3 | ko01210 | 2-Oxocarboxylic acid metabolism | 11 | 0.000604 | 0.018919 |
| ko00010 | Glycolysis / Gluconeogenesis | 13 | 0.000772 | 0.018919 | |
| ko01230 | Biosynthesis of amino acids | 22 | 0.001241 | 0.024325 | |
| ko00300 | Lysine biosynthesis | 5 | 0.003003 | 0.049051 | |
| CK-Y3 vs TY5-3 | ko00190 | Oxidative phosphorylation | 40 | 0.000000 | 0.000010 |
| ko00280 | Valine, leucine and isoleucine degradation | 25 | 0.000146 | 0.003450 | |
| ko00310 | Lysine degradation | 21 | 0.000154 | 0.003450 | |
| ko00071 | Fatty acid degradation | 20 | 0.000175 | 0.003450 | |
| ko00380 | Tryptophan metabolism | 26 | 0.001690 | 0.024933 | |
| CK-Y6 vs TY1-6 | ko00360 | Phenylalanine metabolism | 28 | 0.000006 | 0.000459 |
| ko00380 | Tryptophan metabolism | 34 | 0.000008 | 0.000459 | |
| ko00330 | Arginine and proline metabolism | 34 | 0.000857 | 0.022708 | |
| CK-Y6 vs TY5-6 | ko00270 | Cysteine and methionine metabolism | 31 | 0.000851 |
0.021275 |
| ko00260 | Glycine, serine and threonine metabolism | 36 | 0.002722 |
0.049153 | |
| ko00620 | Pyruvate metabolism | 28 | 0.003539 | 0.049153 |
|
| CK-Y3 vs CK-Y6 | ko01212 | Fatty acid metabolism | 20 | 0.000155 | 0.004560 |
| ko00010 | Glycolysis / Gluconeogenesis | 28 | 0.000756 | 0.014868 | |
| ko00380 | Tryptophan metabolism | 25 | 0.001093 | 0.018430 | |
| ko00310 | Lysine degradation | 18 | 0.001823 | 0.026888 | |
| ko00071 | Fatty acid degradation | 17 | 0.002322 | 0.030442 | |
| ko00520 | Amino sugar and nucleotide sugar metabolism | 25 | 0.004086 | 0.040182 | |
| TY1-Y3 vs TY1-6 | ko01212 | Fatty acid metabolism |
27 | 0.000087 | 0.003112 |
| ko00010 | Glycolysis / Gluconeogenesis | 41 | 0.000154 | 0.003843 | |
| ko00260 | Glycine, serine and threonine metabolism | 42 | 0.000934 | 0.013805 | |
| ko00350 | Tyrosine metabolism | 27 | 0.000982 | 0.013805 | |
| ko00071 | Fatty acid degradation | 24 | 0.000994 | 0.013805 | |
| ko00280 | Valine, leucine and isoleucine degradation | 30 | 0.001707 | 0.021336 | |
| ko00360 | Phenylalanine metabolism | 27 | 0.003465 | 0.039377 | |
| TY5-Y3 vs TY5-6 | ko03008 | Ribosome biogenesis in eukaryotes | 41 | 0.000000 | 0.000000 |
| ko03020 | RNA polymerase | 17 | 0.000011 | 0.000654 |
| NO. | M. ruber PKS cluster | CK-Y3 | TY1-3 | TY5-3 | CK-Y6 | TY1-6 | TY5-6 |
| 1 | Contig6.564 | 3.59 | 4.29 | 3.67 | 4.16 | 15.92 | 4.33 |
| 2 | Contig6.565 | 18.95 |
18.04 |
89.2 |
88.74 |
241.36 |
34.06 |
| 3 | Contig6.566 | 388.7 |
555.47 |
234.37 |
0.76 |
↑2.88 |
↑149.04 |
| 4 | Contig1.632 | 5.4 |
6.17 |
5.9 |
5.81 |
10.96 |
7.92 |
| 5 | Contig6.567 | 698.17 |
1160.71 |
↓202.36 |
1.64 |
3.46 |
↑208.39 |
| 6 | Contig3.926 | 2.34 |
↓1.06 |
↑17.03 |
3.3 |
6.35 |
↓1.55 |
| 7 | Contig9.114 | 84.13 |
↓33.53 |
64.54 |
30.13 |
56.12 |
31.84 |
| 8 | Contig6.568 | 7870.3 |
↑16165. 92 |
3023.02 |
10.64 |
12.76 |
↑4851. 14 |
| 9 | Contig6.569 | 493.42 |
838.2 |
700.63 |
30.01 |
40.42 |
↑340.48 |
| 10 | Contig8.37 | 0.24 |
↑0.71 |
↑0.48 |
0.58 |
↑2.21 |
↑1.67 |
| 11 | Contig6.571 | 2587.31 |
1896.89 |
↓176.57 |
1005.73 |
1101.42 |
↓334.17 |
| 12 | Contig6.572 | 3028.21 |
2036.55 |
↓359.36 |
1632.78 |
2079.7 |
↓623.97 |
| 13 | Contig9.526 | 59.75 |
45.12 |
90.99 |
222.59 |
238.44 |
145.63 |
| 14 | Contig6.573 | 182.56 |
283.66 |
142.07 |
2.04 |
3.32 |
↑90.62 |
| 15 | Contig5.231 | 10.96 |
9.99 |
9.43 |
16.58 |
29.98 |
15.8 |
| 16 | Contig6.574 | 2.95 |
5.77 |
2.68 |
0.8 |
3.52 |
1.97 |
| 17 | Contig1.420 | 37.69 |
55.92 |
154.97 |
27.63 |
31.07 |
70.48 |
| 18 | Contig6.575 | 3.31 |
2.72 |
3.04 |
2.68 |
5.92 |
3.19 |
| 19 | Contig6.576 | 1.03 |
0.34 |
1.03 |
0.89 |
1.36 |
0.88 |
| 20 | Contig2.99 | 2.4 |
2.17 |
1.84 |
2.32 |
5.67 |
2.66 |
| 21 | Contig6.578 | 11.92 |
7.85 |
10.68 |
5.62 |
10.93 |
3.04 |
| 22 | Contig6.579 | 585.88 |
507.92 |
↓219.4 |
0.67 |
↑1.58 |
↑165.35 |
| 23 | Contig6.580 | 2455.46 |
↑4927.89 |
↓718.85 |
2.02 |
↑4.69 |
↑814.05 |
| 24 | Contig6.581 | 863.66 |
1561.22 |
885.15 |
5.57 |
8.95 |
↑579.8 |
| 25 | Contig6.582 | 1142.83 |
1053.13 |
↓245.26 |
241.3 |
348.49 |
298.28 |
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