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Genomic Analysis of an Excellent Wine-Making Strain Oenococcus oeni SD-2a

Longxiang Liu

Longxiang Liu

Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou UniversityBinzhou, China
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Liu, Longxiang
, 
Shuai Peng

Shuai Peng

College of food science and engineering, Gansu Agricultural UniversityLanzhou, China
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Peng, Shuai
, 
Weiyu Song

Weiyu Song

Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou UniversityBinzhou, China
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Song, Weiyu
, 
Hongyu Zhao

Hongyu Zhao

  • College of Enology, Northwest A&F UniversityYangling, China
  • Shaanxi Engineering Research Center for Viti-VinicultureYangling, China
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Zhao, Hongyu
, 
Hua Li

Hua Li

  • College of Enology, Northwest A&F UniversityYangling, China
  • Shaanxi Engineering Research Center for Viti-VinicultureYangling, China
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Li, Hua
 and 
Hua Wang

Hua Wang

  • College of Enology, Northwest A&F UniversityYangling, China
  • Shaanxi Engineering Research Center for Viti-VinicultureYangling, China
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Wang, Hua
  
Jun 19, 2022
Genomic Analysis of an Excellent Wine-Making Strain Oenococcus oeni SD-2a's Cover Image
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Article Category: Original Paper
Published Online: Jun 19, 2022
Page range: 279 - 292
Received: Mar 07, 2022
Accepted: May 14, 2022
DOI: https://doi.org/10.33073/pjm-2022-026
Keywords
© 2022 Longxiang Liu et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
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Fig. 1

Circular map of Oenococcus oeni SD-2a genome. The outermost circle of the circle graph is an indicator of the size of the genome. The second and third circles are genes on positive and negative chains; different colors represent the functional classification of COGs with different genes. The fourth circle is rRNA and tRNA. The fifth circle is GC content; the outward red part indicates that the GC content in this region is higher than the average GC content of the whole genome, the inward blue part indicates that the GC content in this region is lower than the genome-wide average GC content, the higher the peak value, the greater the difference from the average GC content. The innermost circle is the GC skew value; the outward red part indicates that the value is positive, the inward blue part indicates that the value is negative.
Circular map of Oenococcus oeni SD-2a genome. The outermost circle of the circle graph is an indicator of the size of the genome. The second and third circles are genes on positive and negative chains; different colors represent the functional classification of COGs with different genes. The fourth circle is rRNA and tRNA. The fifth circle is GC content; the outward red part indicates that the GC content in this region is higher than the average GC content of the whole genome, the inward blue part indicates that the GC content in this region is lower than the genome-wide average GC content, the higher the peak value, the greater the difference from the average GC content. The innermost circle is the GC skew value; the outward red part indicates that the value is positive, the inward blue part indicates that the value is negative.

Fig. 2

COG function classification of predicted Oenococcus oeni SD-2a proteins. Genes are classified into four main COG functional categories. The number of genes in each category and specific notes on categories are indicated.
COG function classification of predicted Oenococcus oeni SD-2a proteins. Genes are classified into four main COG functional categories. The number of genes in each category and specific notes on categories are indicated.

Fig. 3

Venn diagram showing the number of unique and homologous gene clusters in Oenococcus oeni SD-2a, Oenococcus oeni PSU-1, Oenococcus oeni CRBO-11381, Lactiplantibacillus plantarum UNQLp11, and Pediococcus pentosaceus KCCM40703. The histogram shows each strain’s total gene clusters involved in homologous gene analysis.
Venn diagram showing the number of unique and homologous gene clusters in Oenococcus oeni SD-2a, Oenococcus oeni PSU-1, Oenococcus oeni CRBO-11381, Lactiplantibacillus plantarum UNQLp11, and Pediococcus pentosaceus KCCM40703. The histogram shows each strain’s total gene clusters involved in homologous gene analysis.

Fig. 4

Analysis of collinearity between Oenococcus oeni SD-2a and Oenococcus oeni PSU-1.
Analysis of collinearity between Oenococcus oeni SD-2a and Oenococcus oeni PSU-1.

O_ oeni SD-2a genome statistics information_

Attribute Value
Genome size (bp) 1,989,703
DNA scaffolds 1
Gene number 2,073
Gene total length (bp) 1,738,155
Gene average length (bp) 823
Gene/Genome (%) 87.3
GC content in genome (%) 37.8
rRNA 6
tRNA 41
Prophage 4
Genomic Island 4
CRISPR 0
Language:
English
Publication timeframe:
4 times per year
Journal Subjects:
Life Sciences, Microbiology and Virology
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