Computational protocol: Biodetoxification of toxins generated from lignocellulose pretreatment using a newly isolated fungus, Amorphotheca resinae ZN1, and the consequent ethanol fermentation

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Protocol publication

[…] The selected strains were cultured in the PDA medium, and 8 mg of the dry mycelia were collected. The genomic DNA was extracted using the Qiagen DNeasy Tissue Kit (Qiagen, Valencia, CA, USA) and purified following the "Yeast Genomic DNA Purification Protocol" discussed in the attached handbook. The 18 S rDNA internal transcribed spacer (ITS) sequence was amplified by the universal primers ITS1 (5'-TCCGTAGGTGAACCTGCGG-3') and ITS4 (5'-TCCTCCGCTTAGATATGC-3'). The polymerase chain reaction (PCR) products were purified using the PCR Purification Mini Kit (Omega Biotek, Norcross, GA) and sequenced by Shanghai Biotech Service (Shanghai, China). The ITS sequences were blasted in the National Center for Biotechnology Information database http://www.ncbi.nlm.nih.gov/, and the phylogenetic trees were constructed using Bioedit 7.0 http://www.mbio.ncsu.edu/bioedit/bioedit.html and Mega 4 software http://www.megasoftware.net/ using the neighbor-joining method. […]

Pipeline specifications

Software tools BioEdit, MEGA
Application Phylogenetics
Organisms Triticum aestivum, Oryza sativa, Gossypium hirsutum, Brassica napus
Diseases Callosities
Chemicals Ethanol, Carbohydrates, Carbon