Complete genome sequence data of chitin-degrading Bacillus velezensis RB.IBE29

This work reports the complete genome sequence of chitinolytic Bacillus velezensis RB.IBE29 recently isolated from the rhizosphere of black pepper cultivated in the Central Highlands region of Vietnam. This bacterium had strong antagonistic activity against phytopathogens and possessed a novel chitinase system. The complete genome of strain RB.IBE29 was sequenced using the platforms of Illumina (2×150 PE) and Oxford Nanopore technologies. Assembly showed that strain RB.IBE29 has one 3,957,092-bp circular chromosome with 46.5 % G+C content. DFAST analysis revealed the genome contains 3819 protein-coding genes, 27 rRNAs, 86 tRNAs, 1 tmRNA, 144 pseudogenes, and shares an ANI value of 97.51 % with that of reported B. velezensis NRRL B-41580. The B. velezensis RB.IBE29 genome possesses at least 42 genes concerning heavy metal resistance and plant-growth promotion. CAZymes analysis showed that 103 genes coding for carbohydrate-active enzymes were predicted in the genome, including 41 genes for glycoside hydrolases, 34 genes for glycosyl transferases, 3 genes for polysaccharide lyases, 17 genes for carbohydrate esterases, 6 genes for auxiliary activities, and 2 genes for carbohydrate-binding modules. Of these deduced enzymes, at least 8 probably possess activities against phytopathogens, such as family 18 chitinases, family 16 glucanase, and family 46 chitosanase. AntiSMASH analysis exhibited that 15 biosynthetic gene clusters were found in the genome; among them, 5 show no sequence similarity to known bacterial clusters. The raw sequences in this work were deposited in Mendeley Data. The complete genome sequence of strain RB.IBE29 was submitted to the DDBJ/GenBank/EMBL under accession number AP028932. The obtained data provide insight into the biocontrol ability and plant-growth promotion of B. velezensis RB.IBE29. The data are valuable for further explorations concerning crop production and other fields using gene expression approaches.

genome sequence of strain RB.IBE29 was submitted to the DDBJ/GenBank/EMBL under accession number AP028932.The obtained data provide insight into the biocontrol ability and plant-growth promotion of B. velezensis RB.IBE29.The data are valuable for further explorations concerning crop production and other fields using gene expression approaches. ©

Background
Vietnam is the largest producer and exporter of black pepper in the world.Among the country's regions, the Central Highlands is the capital of black pepper production [1] .B. velezensis RB.IBE29 is a chitinolytic bacterium recently isolated from the rhizospheric soil of black pepper grown in the Central Highlands.In vitro and greenhouse experiments demonstrated that strain RB.IBE29 possesses high chitin-degrading activity and significantly inhibits the mycelial growth of Phytophthora .Field experiments revealed that using B. velezensis RB.IBE29 was a good solution for sustainable black pepper production in this region [2,3] .Strain RB.IBE29 also possesses a novel chitinase system with two family 18 chitinases and an AA10 protein.These chitinases have been expressed in Escherichia coli cells and purified.Purified recombinant chitinases possessed high activities against the spore germination of fungi and the egg-hatching of plant-parasitic nematodes [4,5] .However, the complete genome of this bacterium has yet to be sequenced.This work aimed to sequence and analyze the whole genome of B. velezensis RB.IBE29 to establish a dataset and elucidate its biocontrol ability and plant-growth promotion, as well as open the subsequent studies involved in crop production and related fields.
Analysis revealed that 42 genes concerning heavy metal resistance and plant growth promotion were identified from the B. velezensis RB.IBE29 genome.Among them, 5 genes related to heavy metal resistance, one gene to inorganic phosphate solubilization, 3 genes to inorganic zinc solubilization, 3 genes to inorganic potassium solubilization, 10 genes to Indole-3-acetic acid biosynthesis, 6 genes to nitrate transport and reduction, 5 genes to ACC biosynthesis, and 9 genes to iron uptake and siderophore production ( Table 2 ).In this work, 103 carbohydrate-active enzymes were deduced from the B. velezensis RB.IBE29 genome ( Table 3 ).Of the deduced enzymes, there were 41 glycoside hydrolases, 34 glycosyltransferases, 3 polysaccharide lyases, 17 carbohydrate esterases, 6 auxiliary activities, and 2 carbohydrate-binding modules.Of those, 4 enzymes probably possess antifungal activity against phytopathogens, including one family 16 beta-glucanase, two family 18 chitinases, and one family 46 chitosanase.In addition, 4 genes encoding peptidases (loci RBIBE_22550, RBIBE_36110,  RBIBE_13610, and RBIBE_27440), which possibly exhibit activity against the growth of plant pathogens, were identified from the genome of B. velezensis RB.IBE29.AntiSMASH analysis showed that the genome of B. velezensis RB.IBE29 harbors 14 putative gene clusters responsible for antimicrobial metabolite biosynthesis.Interestingly, 5 clusters show no sequence similarity to known bacterial gene clusters ( Table 4 , Fig. 2 ).

Experimental Design, Materials and Methods
Genomic DNA extraction of B. velezensis RB.IBE29 cells, Illumina library preparation, and sequencing were performed as described by Tran et al. [6] .Libraries for Oxford Nanopore Tech- nologies (ONT) whole genome sequencing were prepared using the Ligation Sequencing Kit (Oxford Nanopore Technologies, USA), following the manufacturer's protocol.The library was then sequenced using a Flongle machine (Oxford Nanopore Technologies, UK) [7] .
De novo assembly, annotation, and bioinformatic analysis of data were done as previously described [6,7] .Briefly, Fastp v.0.23.1 [8] was used to analyze raw sequence reads.Unicycler v.0.4.8 [9] and pipeline flye-medaka-polca [10,11] were used to de novo assemble the analyzed reads.Finally, the web-based annotation pipeline, DFAST [12] , was used to annotate the complete genome sequence of B. velezensis RB.IBE29.An average nucleotide identity analysis (ANI) was analyzed as described previously [13] to determine the genetic relationship of strain RB.IBE29 and known bacteria based on the genome sequence.The carbohydrate-active enzymes database, dbCAN2 metaserver [14] , was used to analyze proteins related to carbon metabolism.The an-tiSMASH v.6.0 [15] was used to predict gene clusters responsible for antimicrobial metabolite biosynthesis.

Limitations
Not applicable.

Ethics Statement
The current work does not involve human subjects, animal experiments, or any data collected from social media platforms.

Fig. 2 .
Fig. 2. Novel biosynthetic gene clusters identified from the Bacillus velezensis RB.IBE29 genome.Note: Biosynthetic gene clusters in the B. velezensis RB.IBE29 complete genome were analyzed using the AntiSMASH.
2023The Author(s).Published by Elsevier Inc.The genomic DNA of B. velezensis RB.IBE29 cells was isolated using the QIAamp DNA mini kit.Genomic libraries for Illumina whole genome sequencing were prepared using the NEBNext Ultra II DNA Library Prep Kit and then sequenced using a MiniSeq machine.Libraries for Oxford Nanopore Technologies whole genome sequencing were prepared using the Ligation Sequencing Kit and then sequenced using a Flongle machine.Finally, bioinformatic tools were used to analyze data.Data can be helpful for comparing the genomics of B. velezensis originating from the Central Highlands and others.•Data can be useful for further explorations involved in agricultural cultivation and other fields using DNA recombinant techniques.

Table 1
Genome features of Bacillus velezensis RB.IBE29.The complete genome features of B. velezensis RB.IBE29 were analyzed using the DFAST.

Table 2
Heavy metal and plant growth-promoting genes found in the Bacillus velezensis RB.IBE29 genome.

Table 2 (
continued ) The heavy metal and plant growth-promoting genes in the B. velezensis RB.IBE29 complete genome were analyzed using the DFAST.

Table 3 (
continued ) Note: The CAZymes in the B. velezensis RB.IBE29 complete genome were analyzed using the dbCAN2 metaserver.

Table 4
Biosynthetic gene clusters found in the Bacillus velezensis RB.IBE29 genome.Biosynthetic gene clusters in the B. velezensis RB.IBE29 complete genome were predicted using the AntiSMASH.