HomeMolecular Plant-Microbe Interactions®Vol. 35, No. 8Genome Sequence Resource of Bacillus velezensis Strain HC-8, a Native Bacterial Endophyte with Biocontrol Potential Against the Honeysuckle Powdery Mildew Causative Pathogen Erysiphe lonicerae var. lonicerae PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseGenome Sequence Resource of Bacillus velezensis Strain HC-8, a Native Bacterial Endophyte with Biocontrol Potential Against the Honeysuckle Powdery Mildew Causative Pathogen Erysiphe lonicerae var. loniceraeWenyan Cui and Pengjie HeWenyan CuiGuizhou University of Traditional Chinese Medicine, Guiyang 550000, Guizhou, ChinaSearch for more papers by this author and Pengjie He†Corresponding author: P. He; E-mail Address: [email protected]http://orcid.org/0000-0003-4379-9126Guizhou University of Traditional Chinese Medicine, Guiyang 550000, Guizhou, ChinaState Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, ChinaSearch for more papers by this authorAffiliationsAuthors and Affiliations Wenyan Cui1 Pengjie He1 2 † 1Guizhou University of Traditional Chinese Medicine, Guiyang 550000, Guizhou, China 2State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China Published Online:13 Jul 2022https://doi.org/10.1094/MPMI-01-22-0021-AAboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Genome AnnouncementBacillus velezensis is a rod-shaped, gram-positive, aerobic, and plant-associated bacterium which encodes approximately 10% of its genome to the synthesis of antimicrobial compounds (i.e., fengycin, surfactin, iturin, bacillaene, difficidin, bacilysin, and macrolactin) (Chen et al. 2009; Chowdhury et al. 2015). As a group of biocontrol bacteria, B. velezensis strains have been widely developed as biocontrol agents that can suppress phytopathogens (Adeniji and Babalola 2019; Islam et al. 2016; Radhakrishnan et al. 2017). These beneficial bacteria have received wide attention as a valuable alternative to chemical fungicides for posing a minimum threat to the environment (Cui et al. 2019a; Huang et al. 2022). Plenty of the B. velezensis species have been isolated from different plants and diverse niches, most of which were isolated from the rhizosphere (Chen et al. 2007; Cui et al. 2019b). As of now, at least 205 complete genome sequences of this species bacteria were available in GenBank (Shi et al. 2022). Among them, the genome sequences of B. velezensis FZB42 was the first one submitted to GenBank in 2007 (Chen et al. 2007).Honeysuckle (Lonicera japonica Thunb., family Caprifoliaceae) is an important herb in traditional Chinese medicine (He et al. 2013; Schierenbeck 2004). Its dried flower buds have been used to treat fever and influenza, especially the SARS-CoV-2 coronavirus (Lee et al. 2021). Powdery mildew caused by Erysiphe lonicerae var. lonicerae is one of the most destructive diseases of honeysuckle (Pigul and Dmitrieva 2013; Rakhimova et al. 2005). Considering honeysuckle's medicinal properties, biocontrol might be a better strategy than use of synthetic chemicals to control honeysuckle powdery mildew (Xiao et al. 2022). In our previous work, B. velezensis strain HC-8 was isolated from the leaves of honeysuckle in China, and showed effective biocontrol activity against E. lonicerae var. lonicerae (He et al. 2021). However, its genomic information was lacking. Here, we describe the complete genome sequence of this bacterium.The genome of B. velezensis strain HC-8 was sequenced to analyze its relatedness to other B. velezensis strains and provide insights into the potential molecular basis of their antifungal activity. The resulting genome sequence data are inestimable for bacteria genomic analysis in comparison with its closest relatives to understand the unique characteristics of strain HC-8 and provide insights into the basis of its antagonism against E. lonicerae var. lonicerae.For sequencing the genome, strain HC-8 was cultured in nutrient broth at 30°C with shaking at 160 rpm for 48 h. Then, bacterial culture was used for genomic DNA extraction by using Hipure Bacteria DNA kits (Magen, Guangzhou, China), following the manufacturer's protocol. The obtained genomic DNA was determined using agarose gel electrophoresis, followed by NanoDrop 2000 spectrophotometry and Qubit assays to evaluate the DNA quality. The whole-genome sequencing of strain HC-8 was performed on both single-molecule real-time (SMRT) cells via Pacific Biosciences Sequel (PacBio, Menlo Park, CA, U.S.A.) and the Illumina Novaseq 6000 sequencer via the paired-end technology (PE 150). After filtration, SMRT sequencing yielded 87,780 subreads with an average length of 16,435.9 bp (total = 1,442,744,760 bp) and an N50 read length of 19,755 bp, providing over 430-fold genome coverage. These subreads were used for de novo assembly to generate one contig without gaps using FALCON (version 0.3.0) (Ardui et al. 2018; Chin et al. 2016). After filtering using FASTP software (version 0.20.0), the resulting clean reads from the Illumina platform were used for correcting the genome sequences of SMRT sequencing to improve the quality of the assembly and determine the final genome sequences using Pilon (version 1.23) (Walker et al. 2014). The completeness of the strain HC-8 genome assembly was assessed using benchmarking universal single-copy ortholog (BUSCO) (version 4.1.4) with bacilli_odb10 as a reference, based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs (Simão et al. 2015). The genome completeness of the BUSCO notation was C: 449 (99.78%) [S: 449, D: 0], F: 1 (0.22%), M: 0, n: 450. Moreover, the taxa assignment of strain HC-8 was evaluated using average nucleotide identity (ANI) analysis (Vanlaere et al. 2009). The ANI value between strain HC-8 and B. velezensis FZB42 was 98.36%, reconfirming that strain HC-8 belongs to the B. velezensis species.Finally, a genome of 4,237,170 bp with a total GC content of 45.85% was finalized as the circular chromosome and deposited in the NCBI database under accession number CP083436.1. Subsequent genome annotation was performed via the NCBI prokaryotic genome annotation pipeline (Tatusova et al. 2016). The genome of strain HC-8 has 4,039 protein-coding sequences, including 498 hypothetical proteins, and 3,541 proteins with functional assignments. Moreover, in total, 86 transfer RNA (tRNA) genes, 27 ribosomal RNA (rRNA) genes, and 19 small RNA genes of the genome were identified by using tRNAscan (version 1.3.1), rRNAmmer (version 1.2), and t cmscan (version 1.1.2), respectively (Lagesen et al. 2007; Lowe and Chan 2016; Nawrocki and Eddy 2013). Furthermore, in total, 73 tandem repeats and 70 interspersed repeats were identified in the genomic sequences. These repeats, in total, accounted for approximately 0.24% in genomes with sizes of 25 to 513 bp. The assembled genome has been deposited in GenBank and the results are summarized in Table 1.Table 1. Genome summary statistics of Bacillus velezensis HC-8Genomic parameterResultsNCBI accessionCP083436Size (bp)4,237,170GC content (%)45.85Number of transposons2Number of repeated sequences143Number of two-component systems28Number of genomic islands5Number of coding sequences4,039Number of RNA genes132Transfer RNAs8616S ribosomal RNA copy numbers9Small RNAs19Hypothetical proteins498Proteins with functional assignments3,541Table 1. Genome summary statistics of Bacillus velezensis HC-8View as image HTML Proteins involved in two-component systems (TCSs) were predicted based on their structural characteristics, which predicted 28 TCSs (total = 56 genes) in the B. velezensis strain HC-8 genome. All of these genes provided important genetic insights into its environmental suitability. As mentioned above, B. velezensis strain HC-8 has significant potential as a biocontrol agent against powdery mildew. The secondary metabolites of fengycin (plipastatin), iturin, and surfactin families of lipopeptide may possess effective antimycotic activities against fungal phytopathogens (Chowdhury et al. 2015; Xu et al. 2013). Gene clusters of secondary metabolites were predicted using antiSMASH (version 4.1.0) (Blin et al. 2017) and revealed 10 potential gene clusters that encode for the biosynthesis of fengycin, surfactin, iturin, bacillibactin, and bacillaene and the antibiotics of polyketides (i.e., difficidin, bacilysin and macrolactin). In conclusion, the B. velezensis HC-8 genome, a native bacterial endophyte of honeysuckle, contains multiple gene clusters predicted to be involved in suppressing phytopathogens, especially against fungal pathogens.To our knowledge, HC-8 is the first strain of B. velezensis species isolated from the medicinal plant honeysuckle (L. japonica Thunb.) for use as potential biocontrol agent reported from China. 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This is an open access article distributed under the CC BY-NC-ND 4.0 International license.DetailsFiguresLiterature CitedRelated Vol. 35, No. 8 August 2022ISSN:0894-0282e-ISSN:1943-7706 Download Metrics Article History Issue Date: 31 Aug 2022Published: 13 Jul 2022Accepted: 1 Apr 2022 Pages: 719-722 InformationCopyright © 2022 The Author(s).This is an open access article distributed under the CC BY-NC-ND 4.0 International license.Funding National Natural Science Foundation of ChinaGrant/Award Number: 32160671 Guizhou Basic Research ProgramGrant/Award Number: ZK[2021]146 Guizhou Science and Technology Support ProgramGrant/Award Number: [2020]4Y099 Administration of Traditional Chinese Medicine of Guizhou ProvinceGrant/Award Number: QZYY-2021-074 KeywordsbiocontrolendophytegenomeLonicera japonica Thunb.The author(s) declare no conflict of interest.PDF downloadCited byComplete Genome Sequence of Bacillus velezensis TH-1, a Candidate Biocontrol Bacterium from ChinaPengjie He, Xiaodi Tang, Shenghua Wei, Jiangyong An, and Wenyan Cui15 February 2023 | Molecular Plant-Microbe Interactions, Vol. 0, No. 0