Genomic and Comparative Transcriptomic Analyses Reveal Key Genes Associated with the Biosynthesis Regulation of Okaramine B in Penicillium daleae NBP-49626
Abstract
:1. Introduction
2. Results
2.1. The Yield Differences of Okaramine B
2.2. Genomic Data Evaluation
2.3. Transcriptomic Data Evaluation
2.4. Differential Expression of Okaramine Biosynthesis Gene Cluster
2.5. Identification of the Differentially Expressed Regulator Genes
2.6. Identification of the DEG Involved in Tryptophan Metabolism
2.7. Identification of the DEG Involved in ATP-Binding Casette (ABC) Transporters
2.8. Validation of RNA-Seq Results by RT-qPCR
3. Discussion
4. Materials and Methods
4.1. Strains and Culture Conditions
4.2. Determination of Okaramine B Production and Mycelial Wet Weight
4.3. Genome DNA Isolation and Sequencing
4.4. Genome Assembly and Gene Annotation
4.5. RNA Isolation and Sequencing
4.6. Analysis of RNA-Seq Data
4.7. Real-Time Quantitative PCR Validation
4.8. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Genome Features | Value |
---|---|
Genome size (bp) | 37,366,436 |
Number of chromosomes | 8 |
N50 scaffold length (bp) | 4,967,589 |
N90 scaffold length (bp) | 2,981,452 |
Maximum scaffold length (bp) | 7,888,045 |
Minimum scaffold length (bp) | 2,295,385 |
G + C content (%) | 49.07 |
Complete BUSCOs of genome (%) | 99.47 |
Number of protein-coding genes | 10,131 |
Avg gene length (bp) | 1663.62 |
Avg CDS length (bp) | 1479.65 |
Average number of exons per gene | 3.24 |
Average exon length (bp) | 456.45 |
Average intron length (bp) | 82.07 |
rRNAs | 58 |
tRNAs | 164 |
Complete BUSCOs of genes (%) | 99.08 |
Number of annotated genes by NR | 9983 |
Number of annotated genes by SWISS-PROT | 7676 |
Number of annotated genes by GO | 6025 |
Number of annotated genes by KEGG | 3514 |
Number of annotated genes by KOG | 3347 |
Number of annotated genes by PHI-base | 2771 |
Number of annotated genes by CAZy | 1435 |
Number of annotated genes by P450 | 177 |
Number of secreted proteins | 715 |
Gene ID | Primer Name | Primer Sequence 5′→3′ |
---|---|---|
4.104 | actin-F | ACAGTCCAAGCGTGGTATCC |
actin-R | CACACGGAGCTCGTTGTAGA | |
3.16 | okaA-F | CTTGATCCGAGCGAGGTTAG |
okaA-R | CGGCTATCGAAGCACTTAGG | |
3.15 | okaB-F | CAAACCAACAAGGCCAAAGT |
okaB-R | TATACCCTCGACCCTCGTTG | |
1.1084 | reg2-F | ACCAGATCAGCTCACCCAAA |
reg2-R | CGATCAAAGCCTGGAACGAG | |
1.213 | reg19-F | TCAGCTCACCAAGTTCCAGT |
reg19-R | CTTCTCGATCTCCTCTGCGT | |
7.557 | try7-F | TGATCTCTGGTGCCCTCAAG |
try7-R | GCTGGCTTAGAGTTACCCCA | |
5.320 | try9-F | CTTCTGTGGAAACTCGCTGG |
try9-R | ACAAACACCAATGGAAGCCC | |
2.1634 | trans4-F | GCACTGTTGAGCGAAAGGAA |
trans4-R | TGTTTCAGGTTGGTGGCATG | |
2.896 | trans5-F | TCCTTGCTCGTTCCCTCATT |
trans5-R | AGTACATCCACGACTGCCAA |
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Wang, Y.; Chen, L.; Fang, W.; Zeng, Z.; Wu, Z.; Liu, F.; Liu, X.; Gong, Y.; Zhu, L.; Wang, K. Genomic and Comparative Transcriptomic Analyses Reveal Key Genes Associated with the Biosynthesis Regulation of Okaramine B in Penicillium daleae NBP-49626. Int. J. Mol. Sci. 2024, 25, 1965. https://doi.org/10.3390/ijms25041965
Wang Y, Chen L, Fang W, Zeng Z, Wu Z, Liu F, Liu X, Gong Y, Zhu L, Wang K. Genomic and Comparative Transcriptomic Analyses Reveal Key Genes Associated with the Biosynthesis Regulation of Okaramine B in Penicillium daleae NBP-49626. International Journal of Molecular Sciences. 2024; 25(4):1965. https://doi.org/10.3390/ijms25041965
Chicago/Turabian StyleWang, Yueying, Ling Chen, Wei Fang, Zhen Zeng, Zhaoyuan Wu, Fang Liu, Xiaoyan Liu, Yan Gong, Lei Zhu, and Kaimei Wang. 2024. "Genomic and Comparative Transcriptomic Analyses Reveal Key Genes Associated with the Biosynthesis Regulation of Okaramine B in Penicillium daleae NBP-49626" International Journal of Molecular Sciences 25, no. 4: 1965. https://doi.org/10.3390/ijms25041965