Complete Genome Sequence Data of a Newly Isolated Streptomyces violascens Strain A10, a Potential Biological Control Agent for Fungal and Oomycete Diseases

HomePlant DiseaseVol. 106, No. 9Complete Genome Sequence Data of a Newly Isolated Streptomyces violascens Strain A10, a Potential Biological Control Agent for Fungal and Oomycete Diseases PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseComplete Genome Sequence Data of a Newly Isolated Streptomyces violascens Strain A10, a Potential Biological Control Agent for Fungal and Oomycete DiseasesShun Feng, Pan Dong, Liang Jin, and Zhengguo LiShun Fenghttps://orcid.org/0000-0002-0273-8813School of Horticulture, Hainan University, Haikou 570228, ChinaKey Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, ChinaSearch for more papers by this author, Pan Donghttps://orcid.org/0000-0003-1859-0478Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, ChinaSearch for more papers by this author, Liang Jin†Corresponding authors: L. Jin; E-mail Address: jinlia6602@cqu.edu.cn, and Z. Li; E-mail Address: zhengguoli@cqu.edu.cnKey Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, ChinaSearch for more papers by this author, and Zhengguo Li†Corresponding authors: L. Jin; E-mail Address: jinlia6602@cqu.edu.cn, and Z. Li; E-mail Address: zhengguoli@cqu.edu.cnKey Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, ChinaSearch for more papers by this authorAffiliationsAuthors and Affiliations Shun Feng1 2 Pan Dong2 Liang Jin2 † Zhengguo Li2 † 1School of Horticulture, Hainan University, Haikou 570228, China 2Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China Published Online:27 Jul 2022https://doi.org/10.1094/PDIS-11-21-2561-AAboutSectionsView articlePDFSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat View articleGenome AnnouncementPotato is the third largest food crop in the world (Nicolia et al. 2015) but it encounters a variety of diseases such as late blight and Fusarium wilt during its growth (Axel et al. 2012; Glare et al. 2012). Although chemical pesticides can effectively inhibit plant pathogens, environmental pollution and food safety problems caused by long-term and large-scale application of chemical pesticides have prompted people to look for environmentally friendly alternative measures such as biological control (Glare et al. 2012; Rigling and Prospero 2018). Studies have shown that Streptomyces spp. can produce a variety of secondary metabolites (such as antibiotics, cell wall degrading enzymes, volatile substances, and so on) with antimicrobial activity (Viaene et al. 2016; Worsley et al. 2020), suggesting that Streptomyces spp. have great potential to become biological control agents (BCAs).In the early stage of this study, several actinomycetes antagonistic to late blight were isolated from the potato rhizosphere (Feng et al. 2021b). Among them, strain A10 was identified as a new isolate of Streptomyces violascens based on 16S ribosomal RNA (rRNA) sequence and whole-genome sequence alignment (Supplementary Fig. S1; Supplementary Table S1), and it could inhibit the growth of Botrytis cinerea, Fusarium oxysporum, and Phytophthora infestans. Strain A10 was deposited in China General Microbiological Culture Collection Center, with the deposit number of CGMCC 2116 (https://cgmcc.net/). The growth of A10 on seven ISP plates was examined. Aerial mycelia of A10 were observed on most of the media plates, which were white or light yellow, and no pigment was observed (Supplementary Fig. S2). Previous studies on S. violascens have mainly focused on the separation of various enzymes (such as chitinase, lipase, and cholesterol oxidase) and other novel metabolites (Gao et al. 2020; Zheng et al. 2017) but have ignored its potential for use in biocontrol. We found that strain A10 had broad-spectrum antifungal activity in vitro and showed excellent biological control effect on tomato gray mold, potato late blight, Fusarium wilt, and dry rot (unpublished data). This study sequenced the whole genome of A10, which would contribute to predicting the potential and mechanism of A10 as a BCA from the genomic level.According to the method of Feng et al. (2021a), strain A10 was cultured and its DNA was extracted for whole-genome sequencing. Whole-genome sequencing was performed at the Shanghai Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China) based on the Illumina 415 HiSeq X 10 System (Illumina) and PacBio RS II (Pacific Biosciences). For Illumina sequencing, a 550-bp short-insert library was constructed. For PacBio sequencing, sequence runs for single-molecule real-time cells were carried out. After the raw data were filtered, 458,536 subreads (N50 value = 157,181) with an average length of 9,178 bp (total = 4,208,758,195 bp) were obtained. De novo assembly of the genome was conducted using SPAdes version 3.12 (Hyatt et al. 2010), which assembles PacBio and Illumina sequences together. After assembly, no plasmid sequences were identified. Rapid annotation subsystem technology (NCBI Prokaryotic Genome Annotation Pipeline) was used to predict protein-coding genes, transfer RNAs (tRNAs), and rRNAs (Overbeek et al. 2014). The gene clusters involved in secondary metabolite production were annotated with antiSMASH 4.0.2 (https://antismash.secondarymetabolites.org/) and carbohydrate-active enzymes (CAZymes) were annotated with the CAZymes 6.0 (http://www.cazy.org/) database (Cui et al. 2020; Yin et al. 2012).The final assembled genome of A10 consisted of one DNA chromosome of 6,984,675 bp with a GC 73.43% content and no plasmid, including 67 tRNA genes, 21 rRNA genes and 5,788 protein-coding genes (Supplementary Table S2). Total of 17 auxiliary activities, 4 carbohydrate-binding modules, 50 carbohydrate esterases, 74 glycoside hydrolases, 39 glycosyl transferases, and 2 polysaccharide lyases were identified (Supplementary Table S3). AntiSMASH functional analysis found that strain A10 has 21 secondary metabolite biosynthesis gene clusters (Table 1). A10 shared 100% similarity with some known secondary biosynthesis gene clusters, which encoded antimicrobial activities substances such as albaflavenone (Gil and Campelo-Diez 2003; Liu et al. 2019), candicidin (Gürtler et al. 1994; Moody et al. 2012), SAL-2242 (lanthipeptides) and SGR_PTMs (t1pks-nrps) (Fisch 2013; Repka et al. 2017). In addition, A10 shared 100% similarity with the growth-promoting substance Desferrioxamine_B biosynthesis gene cluster. Desferrioxamine_B is a linear trihydroxamic acid siderophore and it can inhibit metal ion-dependent processes essential to bacteria or deliver exogenous antibiotics as siderophore-antibiotic conjugates using native siderophore uptake mechanisms, making them available to the plant (Zhang et al. 2020). Siderophores play a role in the biocontrol of plant diseases by causing iron starvation of phytopathogens, thus fostering successful competition by biocontrol agents (Kramer et al. 2020). For instance, Burkholderia pyrrocinia JK-SH007 enhanced cucumber (Cucumis sativus) and tomato (Lycopersicon esculentum) growth via siderophore mediation (Min et al. 2020). What’s more, A10 shared 100% similarity with the microbial cytoprotectant ectoine, which helped to improve competitive advantage. Ectoine is a broadly synthesized and highly effective microbial cytoprotectant during osmotic stress and high or low growth temperature extremes (Hermann et al. 2020; Tsai et al. 2020); hence, these metabolites may play a critical role in environmental stress tolerance improvement (Cañamás et al. 2007).Table 1. Secondary metabolite synthesis gene clusters in A10 genome predicted by antiSMASHaCluster IDTypeSimilar clusterSimilarity to known BGC (%)Cluster1Terpene-nrpsLividomycin BGC, saccharide10Cluster2t1pks-nrpsSGR_PTMs BGC, hybrid100Cluster3TerpeneHopene BGC, terpene76Cluster4Bacteriocin−−Cluster5Bacteriocin−−Cluster6nrpsTetronasin BGC, polyketide9Cluster7Siderophore−−Cluster8TerpeneKanamycin BGC, saccharide1Cluster9TerpeneAlbaflavenone BGC, terpene100Cluster10Thiopeptide−−Cluster11LantipeptideSAL-2242 BGC, RiPP100Cluster12nrpsMannopeptimycin BGC, nrps51Cluster13nrpsScabichelin BGC, nrps40Cluster14nrpsDesotamide BGC, nrps13Cluster15nrps−−Cluster16SiderophoreDesferrioxamine_B BGC, other100Cluster17EctoineEctoine BGC, other100Cluster18OtherIndigoidine BGC, nrps80Cluster19Bacteriocin-terpeneCarotenoid BGC, terpene54Cluster20t3pksHerboxidiene BGC, polyketide12Cluster21Lantipeptide-t1pks-nrpsCandicidin BGC, polyketide100aBGC = biosynthetic gene clusters.Table 1. Secondary metabolite synthesis gene clusters in A10 genome predicted by antiSMASHaView as image HTML In all, 21 secondary metabolite biosynthesis gene clusters and 186 CAZymes were identified in the genome, which would encode many antimicrobial substances to inhibit fungal and oomycete diseases. This genome sequence could provide new molecular biology basis and insights into the biocontrol activity of S. violascens. The gene cluster information about antimicrobial substances, growth-promoting substances, and microbial cytoprotectants suggests that A10 may carry out biological control of plant diseases through a variety of ways. It may contribute to investigations of the molecular basis underlying the biocontrol activity of S. violascens strain A10.Data AvailabilityThe complete genome sequence of S. violascens strain A10 has been deposited in the GenBank via the NCBI under accession number CP063844 (PRJNA672183 and SAMN16560567).The raw data were deposited in the NCBI Sequence Read Archive under accession SRA: SRR16998463.AcknowledgmentsWe thank Z. Wang (School of Life Sciences, Chongqing University) for help with the microbiology guidance.The author(s) declare no conflict of interest.Literature CitedAxel, C., Zannini, E., Coffey, A., Guo, J. H., Waters, D. M., and Arendt, E. K. 2012. Ecofriendly control of potato late blight causative agent and the potential role of lactic acid bacteria: A review. Appl. Microbiol. Biotechnol. 96:37-48. https://doi.org/10.1007/s00253-012-4282-y Crossref, ISI, Google ScholarCañamás, T. P., Viñas, I., Usall, J., Magan, N., Morelló, J. R., and Teixidó, N. 2007. 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Prod. 80:837-844. https://doi.org/10.1021/acs.jnatprod.6b00676 Crossref, ISI, Google ScholarFunding: This work was supported by Chongqing Natural Science Foundation (cstc2019jcyj-msxmX0127) and Fundamental Research Funds for the Central Universities (2021CDJZYJH-002).The author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 106, No. 9 September 2022SubscribeISSN:0191-2917e-ISSN:1943-7692 Download Metrics Article History Issue Date: 30 Aug 2022Published: 27 Jul 2022Accepted: 1 Apr 2022 Pages: 2498-2501 Information© 2022 The American Phytopathological SocietyFundingChongqing Natural Science FoundationGrant/Award Number: cstc2019jcyj-msxmX0127Fundamental Research Funds for the Central UniversitiesGrant/Award Number: 2021CDJZYJH-002KeywordsbiocontrolBotrytis cinereagenomicspotato diseaseStreptomyces violascensThe author(s) declare no conflict of interest.PDF download