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. 2022 Jun 19;71(2):279-292.
doi: 10.33073/pjm-2022-026.

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

Longxiang Liu  1 , Shuai Peng  2 , Weiyu Song  1 , Hongyu Zhao  3   4 , Hua Li  3   4 , Hua Wang  3   4
Affiliations

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

Longxiang Liu et al. Pol J Microbiol. .

Abstract

Oenococcus oeni is an important microorganism in wine-making-related engineering, and it improves wine quality and stability through malolactic fermentation. Although the genomes of more than 200 O. oeni strains have been sequenced, only a few include completed genome maps. Here, the genome sequence of O. oeni SD-2a, isolated from Shandong, China, has been determined. It is a fully assembled genome sequence of this strain. The complete genome is 1,989,703 bp with a G+C content of 37.8% without a plasmid. The genome includes almost all the essential genes involved in central metabolic pathways and the stress genes reported in other O. oeni strains. Some natural competence-related genes, like comEA, comEC, comFA, comG operon, and comFC, suggest that O. oeni SD-2a may have natural transformation potential. A comparative genomics analysis revealed 730 gene clusters in O. oeni SD-2a homologous to those in four other lactic acid bacteria species (O. oeni PSU-1, O. oeni CRBO-11381, Lactiplantibacillus plantarum UNQLp11, and Pediococcus pentosaceus KCCM40703). A collinearity analysis showed poor collinearity between O. oeni SD-2a and O. oeni PSU-1, indicating great differences in their evolutionary histories. The results provide general knowledge of O. oeni SD-2a and lay the foundation for specific gene function analyses.

Keywords: Oenococcus oeni SD-2a; collinearity; genome; homologous genes.

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Conflict of interest statement

Conflict of interest

The authors do not report any financial or personal connections with other persons or organizations, which might negatively affect the contents of this publication and/or claim authorship rights to this publication.

Figures

Fig. 1
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.
Fig. 2
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.
Fig. 3
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.
Fig. 4
Fig. 4
Analysis of collinearity between Oenococcus oeni SD-2a and Oenococcus oeni PSU-1.
None
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Supplementary concepts

Grants and funding

This work was supported by the National Natural Science Foundation of China (No.32001659), Shandong Natural Science Foundation of Youth project (ZR2020QC224), the National Natural Science Foundation of China (No. 31471708) and Science and Technology Support Plan for Youth Innovation of Colleges and Universities in Shandong Province (2020KJD005).

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