Complete genome sequence of Bacillus velezensis YYC, a bacterium isolated from the tomato rhizosphere

The Bacillus velezensis YYC strain was isolated from the tomato rhizosphere. In a previous experiment, it increased tomato growth and induced systemic resistance against Ralstonia solanacearum. However, information on its genomic content is lacking. The complete genome sequence of the bacterium was described in this study. The genome size was 3,973,236 bp and consisted of 4034 genes in total, with a mean G + C content of 46.52%. In addition, 86 tRNAs and 27 ribosomal RNAs were identified. Fourteen clusters of secondary metabolites were identified. The KEGG database analysis showed that 69 genes were related to quorum sensing, which were important for microbe-plant interaction. In addition, genes involved in promoting plant growth and triggering plant immunity were identified from the genome. Based on digital DNA–DNA hybridizations (dDDH), B. velezensis YYC was most closely related with B. velezensis FZB42. The complete genome data of B. velezensis YYC will provide a basis for explanation of its growth-promoting mechanism and biocontrol mechanism.


Introduction
Bacillus velezensis is an important member of plant growthpromoting rhizobacteria (PGPR). PGPR promotes plant growth by nitrogen fixation, solubilization of phosphates or antagonists to soil-borne disease (Canellas et al. 2013). In addition, some strains of B. velezensis were known to have growth-promoting effects and produce a variety of secondary metabolites with antifungal or antibacterial activity (Chowdhury et al. 2015). For example, B. velezensis 5YN8 and DSN012 can significantly control the phytopathogenic fungus Botrytis cinerea by secreting some secondary metabolites and promote the pepper growth (Jiang et al. 2018). B. velezensis FJAT-46737 controls the tomato bacterial wilt by secreting of lipopeptides (Chen et al. 2020). B. velezensis can be widely isolated from diversified environments, such as plant rhizospheres, soil, rivers, human food, animal guts and seawater, and can easily be isolated and cultured (Ye et al. 2018). In our work, the rhizosphere soil of tomato was used to isolate the strain YYC in Qiqihar University Botanical Garden of Heilongjiang in China. Alexandrov medium was used to isolate bacteria from rhizosphere soil of tomato. B. velezensis YYC increased tomato growth and induced systemic resistance against Ralstonia solanacearum (unpublished data). Strain YYC is a non-pathogenic bacterium. Genome sequencing of B. velezensis YYC will provide basic insight into the growth-promoting and biocontrol mechanism.
1 3 44 Page 2 of 5 smpB, tsf), it was identified as Bacillus velezensis. Bacterial genomic DNA extraction kit (Majorbio Bio-pharm Technology Co., Ltd., Shanghai, China) was used to extract genomic DNA. A TBS-380 fluorometer (Turner Bio-Systems Inc., Sunnyvale, CA) was used to quantify the purified genomic DNA. PacBio RS II Single Molecule Real Time (SMRT) and Illumina sequencing platforms were used to sequence the genomic DNA. The sequencing yielded 170,436 reads, including 1,341,760,841 bp, with 337.7 × sequence depth. A statistical technology of quality information was applied for quality trimming, by which the low-quality data could be removed to result in clean data. Using Unicycler (Version 0.4.7) with both Illumina and PacBio data (Wick et al. 2017), the reads were assembled into contigs. A complete genome was generated by inspecting and completing the last circular step. Finally, using the Illumina reads, error correction of the PacBio assembly results was performed.

General genome features of B. velezensis YYC
Whole-genome sequencing showed that the B. velezensis YYC strain contained a genome size of approximately 3,973,236 bp, with an average G + C content of 46.52%. The GeneMarkS program predicted that the number of protein coding sequences (CDSs) was 3779. Furthermore, a total of 86 tRNA and 27 ribosomal RNA genes were identified in the genome. By aligning the genome to sequences from diverse databases, including the NR, KEGG, GO and COG databases, the numbers of identified genes were 4034, 2163, 2668 and 3013, respectively.
Sixty-one genes were associated with chemotaxis by querying the NR database, which plays a significant role during the rhizosphere colonization by rhizobacteria (Feng et al. 2021). And the KEGG database analysis showed a great number of two-component systems (113 genes) and ABC transporters (117 genes). At the same time, 69 genes were related to quorum sensing, which were important for microbe-plant interactions (Kan et al. 2017). The GO database analysis showed that 1483 genes were associated with molecular function of binding, which may be helpful to its plant colonization (Zeng et al. 2020). Furthermore, the COG database showed a great number of cell wall and membrane biosynthesis (180 genes), bacterial mobility (38 genes) and secondary metabolites biosynthesis (79 genes), which were important for the strain's biocontrol, colonization, and stimulation of plant growth (Guo et al. 2015) (Fig. 1).

Secondary metabolites related to biocontrol
AntiSMASH version 6.0.1 analysis identified 14 clusters of secondary metabolites (Fig. 1). Six clusters of secondary metabolites were related to the synthesis of plantazolicin, macrolactin H, bacillaene, fengycin, difficidin and bacilysin, which can directly inhibit the growth of fungi and bacteria (Chowdhury et al. 2015). In addition, fengycin was found to induce resistance to plant diseases and suppress Sclerotinia sclerotiorum (Farzand et al. 2019).

Genes involved in promoting plant growth and triggering plant immunity
Some strains could colonize the rhizosphere of the plant, promote plant growth and elicit plant defenses . In addition to producing secondary metabolites with antifungal or antibacterial activity, B. velezensis YYC contains various of genes involved in root colonization and biofilm formation, such as sacB and spo0A (Bezzate et al. 2000;Branda et al. 2001) (Table 2). In addition, the moaA (encoding molybdenum cofactor biosynthesis protein A) was found in the YYC genome, which may be related to nitrogen assimilation (Bird et al. 2003). It also contains the genes encoding acetolactate synthase (ilvH, ilvB), acetolactate decarboxylase (alsD), and butanediol dehydrogenase (butB), which have plant growth-promoting effects including stimulating root formation and increasing systemic disease resistance (He et al. 2013;Jayakumar et al. 2021). B. velezensis YYC also has the genes required for synthesis of 2, 3-butanediol (alsD), the compound reported to trigger systemic resistance (He et al. 2013).
The strain was stored in China Center for Type Culture Collection (CCTCC) in Wuhan with the accession number of CCTCC M 20,211,227.