An Optimized Method for the Preparation of Monascus purpureus DNA for Genome Sequencing

Abstract:

More and more attention has been paid to filamentous fungal evolution, metabolic pathway and gene functional analysis via genome sequencing. However, the published methods for the extraction of fungal genomic DNA were usually costly or inefficient. In the present study, we compared five different DNA extraction protocols: CTAB protocol with some modifications, benzyl chloride protocol with some modifications, snailase protocol, SDS protocol and extraction with the E.Z.N.A. Fungal DNA Maxi Kit (Omega Bio-Tek, USA). The CTAB method which we established with some modification in several steps is not only economical and convenient, but also can be reliably used to obtain large amounts of highly pure genomic DNA from Monascus purpureus for sequencing with next-generation sequencing technologies (Illumina and 454) successfully.

• Periodical: Applied Mechanics and Materials (Volume 563)
• Pages: 379-383
• DOI: https://doi.org/10.4028/www.scientific.net/AMM.563.379
• Online since: May 2014
• Authors: Yue Yang, Xin Jun Du, Ping Li, Bin Liang, Shuo Wang*
• Keywords: DNA Extraction, Genomics, Monascus purpureus

References

[1] L. Li, Y. C. Shao, Q. Li, S. Yang, F. S. Chen, Identification of Mga1, a G-protein alpha-subunit gene involved in regulating citrinin and pigment production in Monascus ruber M7, FEMS Microbiol. Lett. 308 (2010) 108-114.

DOI: 10.1111/j.1574-6968.2010.01992.x

[2] Y. C. Shi, T. M. Pan, Beneficial effects of Monascus purpureus NTU 568-fermented products: a review, Appl. Microbiol. Biotechnol. 90 (2011) 1207-1217.

DOI: 10.1007/s00253-011-3202-x

[3] S. A. Mapari, U. Thrane, A. S. Meyer, Fungal polyketide azaphilone pigments as future natural food colorants? Trends Biotechnol. 28 (2010) 300-307.

DOI: 10.1016/j.tibtech.2010.03.004

[4] Y. Feng, Y. C. Shao, F. S. Chen, Monascus pigments, Appl. Microbiol. Biotechnol. 96 (2012) 1421-1440.

DOI: 10.1007/s00253-012-4504-3

[5] A. Endo, Monacolin K, a new hypocholesterolemic agent produced by Monascus species, J. Antibiot. 32 (1979) 852-854.

DOI: 10.7164/antibiotics.32.852

[6] Y. P. Chen, C. P. Tseng, L. L. Liaw, C. L. Wang, I. C. Chen, W. J. Wu, M. D. Wu, G. F. Yuan, Cloning and characterization of monacolin K biosynthetic gene cluster from Monascus pilosus, J. Agric. Food. Chem. 56 (2008) 5639-5646.

DOI: 10.1021/jf800595k

[7] H. Takahashi, M. Tiba, T. Yamazaki, F. Noguchi, On the site of action of γ-aminobutyric acid on blood pressure, Jpn. J. Physiol. 8 (1958) 378-390.

DOI: 10.2170/jjphysiol.8.378

[8] T. Shimizu, H. Kinoshita, S. Ishihara, K. Sakai, S. Nagai, T. Nihira, Polyketide synthase gene responsible for citrinin biosynthesis in Monascus purpureus, Appl. Environ. Microbiol. 71 (2005) 3453-3457.

DOI: 10.1128/aem.71.7.3453-3457.2005

[9] T. Shimizu, H. Kinoshita, T. Nihira, Identification and in vivo functional analysis by gene disruption of ctnA, an activator gene involved in citrinin biosynthesis in Monascus purpureus, Appl. Environ. Microbiol. 73 (2007) 5097-5103.

DOI: 10.1128/aem.01979-06

[10] B. M. Pryor, R. L. Gilbertson, Molecular phylogenetic relationships amongst Alternaria species and related fungi based upon analysis of nuclear ITS and mt SSU rDNA sequences, Mycol. Res. 104 (2000) 1312-1321.

DOI: 10.1017/s0953756200003002

[11] M. A. Saghai-Maroof, K. M. Soliman, R. A. Jorgensen, R. W. Allard, Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, andpopulation dynamics, Proc. Natl. Acad. Sci. U. S. A. 81 (1984) 8014-8018.

DOI: 10.1073/pnas.81.24.8014

[12] H. Zhu, F. Qu, L. H. Zhu, Isolation of genomic DNAs from plants, fungi and bacteria using benzyl chloride, Nucleic. Acids. Res. 21 (1993) 5279-5280.

DOI: 10.1093/nar/21.22.5279

[13] E. A. Duell, S. Inoue, M. F. Utter, Isolation and properties of intact mitochondria from spheroplasts of yeast, J. Bacteriol. 88 (1964) 1762-1773.

DOI: 10.1128/jb.88.6.1762-1773.1964

[14] Y. An, J. Yang, X. X. Xu, G. Liu, Construct cosmid libraries by isolating large genomic DNA fragments from Monascus rubber, Acta. Microbiologica. Sinica. 49 (2009) 1385-1388.

[15] Y. C. Kim, S. L. Morrison, A rapid and economic in-house DNA purification method using glass syringe filters, PLoS One 4 (2009) e7750.

DOI: 10.1371/journal.pone.0007750

[16] Z. Q. Zhang, M. Ishaque, Evaluation of methods for isolation of DNA from slowly and rapidly growing mycobacteria, Int. J. Lepr. Other. Mycobact. Dis. 65 (1997) 469-476.

[17] J. T. Belisle, M. G. Sonnenberg, Isolation of genomic DNA from mycobacteria, Methods in Mol. Biol. 101 (1998) 31-44.

DOI: 10.1385/0-89603-471-2:31

[18] J. Odumeru, A. Gao, S. Chen, M. Raymond, L. Mutharia, Use of the bead beater for preparation of Mycobacterium paratuberculosis template DNA in milk, Can. J. Vet. Res. 65 (2001) 201-205.

DOI: 10.1016/j.mimet.2006.10.019

[19] N. R. Morris, Preparation of large molecular weight DNA from the fungus Aspergillus nidulans, J. Gen. Microbiol. 106 (1978) 387-389.

DOI: 10.1099/00221287-106-2-387

[20] B. W. Bainbridge, C. L. Spreadbury, F. G. Scalise, J. Cohen, Improved methods for the preparation of high molecularweight DNA from large and small scale cultures of filamentous fungi, FEMS Microbiol. Lett. 54 (1990) 113-117.

DOI: 10.1111/j.1574-6968.1990.tb03981.x