Open Access Highly Accessed Research article

Genome sequencing and genetic breeding of a bioethanol Saccharomyces cerevisiae strain YJS329

Dao-Qiong Zheng, Pin-Mei Wang, Jie Chen, Ke Zhang, Tian-Zhe Liu, Xue-Chang Wu*, Yu-Dong Li* and Yu-Hua Zhao

Author Affiliations

Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, P R China

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BMC Genomics 2012, 13:479  doi:10.1186/1471-2164-13-479

Published: 15 September 2012

Additional files

Additional file 1:

Comparison of fermentation rates (CO2production) of YJS329 (cycle) and BYZ1 (triangle). Fermentations were performed under (A) regular, (B) heat, and (C) high-gravity conditions motioned in the section of Material and Methods.

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Additional file 2:

Comparison of the regions with copy number variations (CNVs) between YJS329 and BYZ1.

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Additional file 3:

Verification of the amplification of the DNA region of chromosome 4 in BY4742 genome. Two pairs of primers (sequences were showed in Additional file 15) specified to genes HMO1 and UME6 were designed to verify the copy number variations of the ~60 kb region of chromosome 4 in BY4741, YJS329, and BY4742 genomes by RT-qPCR.

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Additional file 4:

Comparison of ethanol yield of YJS329 and YJSH1. Fermentations were performed under regular, high gravity, and heat conditions described in the Methods.

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Additional file 5:

Status and distribution of polymorphisms in each of the YJS329 chromosomes.

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Additional file 6:

Details of the sequence variations detected in the YJSH1 genome.

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Additional file 7:

Details of the YJSH1gene annotations.

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Additional file 8:

RNA-seq reads mapping to S288c genome and genes.

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Additional file 9:

Differentially expressed genes of YJS329 and BYZ1 revealed by RNA-Seq.

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Additional file 10:

Functional classification and transcriptional-regulation analysis of genes expressed differently in BYZ1 and YJS329. (A) GO functional enrichment analysis of genes expressed differently in BYZ1 and YJS329 (FDR < 0.05). Orange pillars represent the classification of up-regulated genes in YJS329, and olive pillars represent the down-regulated genes. (B) Regulation network analysis of some key trans-transcriptional factors and their target genes. These genes were grouped into five terms marked with different color borders, including trehalose metabolism (black), antioxidative factors (green), heat-shock proteins (red), and fatty-acid and ergosterol metabolism (blue). Regulation relationships are presented by the arrows linking the nodes. The genes up-regulated or down-regulated genes with respect to BYZ1 are shown in red and green, respectively, and the color gradient represents the extent of regulation.

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Additional file 11:

Comparison of the expression levels of stress-related genes between BYZ1 and YJS329.

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Additional file 12:

The different efficiencies of the promoters of HSF1, SFA1 , and ALD6 between BYZ1 and YJS329. The efficiency of the promoters was evaluated by the expression activity of report gene Cre. The values were represented by log2 ratio of YJS329/BYZ1. Error bars represent SD of three independent samples. Format: DOC.

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Additional file 13:

The effects of ALD6 deletion on metabolites yield of ethanol fermentation. Yeast cells were precultured in YPD overnight, and were then transferred to the fermentation medium (10/L yeast extract, 20 g/L peptone, and 160 g/L glucose) with the initial OD600 of 1. Fermentations were performed at 30°C for 55 h.)

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Additional file 14:

Verification of the transcription of some novel genes. (A) The expression level and boundary of the novel ORF chr06.003. (B) Relative expression of five novel ORFs under different conditions. YJS329 was grown in YPD medium with initial OD600 of 0.05, and total RNA were then extracted at 7 h (exponential phase), 15 h (diauxic growth), and 25 h (stationary) for determination of the expression of these novel genes. "Fermentation" indicates the total RNA extracted at 20 h under ethanol-fermentation conditions (33°C) with corn mash as the feedstock (containing 270 g/L glucose.)

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Additional file 15:

Primers used in this study.

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