Tomato is the second mostly consumed plant produce worldwide with wide range of pharmaceutically valuable secondary metabolites (Quinet et al. 2019). Sequencing of this Streptomyces sp. genome results in 7,670,883 reads representing 8.18 Mb genome with an average GC content of 72.61 %. The genome was assembled from 32 scaffolds (containing 7,207,566 bp) with N50s of 592,385 bp. The details of the genome were tabulated in Table 1. Similar kind of genome results recorded in Streptomyces avermitilis contains 9,025,608 bases average GC content, 70.7% (Ikeda et al. 2003). Whole genome sequencing (WGS) is a complete requirement for the modern natural product discovery for the agricultural, biomedical and pharmaceutical products.
Table 1
Genome details of the Streptomyces sp. VITGV156
Features | Streptomyces sp. VITGV156 |
Genome size (bp) | 8.18 Mb |
Total number of bases sequenced | 7,207,566 bp |
GC content | 72.61 |
Total genes | 6,386 |
ANI value Streptomyces luteus strain TRM45540 (%) | 91.22 |
dDDH value Streptomyces luteus strain TRM45540 (%) | 44.00 |
Genes with no blast hit | 151 |
Protein coding genes | 6,259 |
rRNA operons | 5 |
tRNA operons | 81 |
A representative genome map was drawn using CGViewer server V1.0. Schematic circular representation of genome sequences for strain Streptomyces sp. VITGV156 (Fig. 1). Genome map of Streptomyces sp. VITGV156, open reading frames with GC skew and GC content was highlighted in the map. The outer circlels from first to third circle shows the positions of the ORF genes in clockwise and from fourth to six counter-clockwise directions, respectively. The seventh circle shows GC skew (higher than average GC content in green, lower than average in purple) and the second innermost circle shows the GC content of the entire genome sequence. The innermost circle shows the size of the genome Streptomyces sp. VITGV156. Chen et al. (2019) report shows similar circular representation of the ORF, GC skew, GC content and genome size in the strain Streptomyces sp. S063 complete genome. Phylogenetic analysis performed using 16s ribosomal RNA sequences revealed the uniqueness of this strain. The 16s rRNA gene sequence of Streptomyces sp. VITGV156 has been deposited in NCBI GenBank (Accession ID – MZ750937). In phylogenetic tree, Streptomyces sp. VITGV156 falls on a separate branch which shows its distinct nature. BLAST analysis shows similarity with Streptomyces luteus (99%), Streptomyces mutabilis (99%), Streptomyces enissocaesilis (99%), Streptomyces minutiscleroticus (99%), Streptomyces rochei (99%), and Streptomyces tuirus (99%). This result is in accordance with previous analytical report of Kim and Goodfellow (2002) in Streptomyces avermitilis sp. nov.
The results of the comparative genome analysis with neighbour Streptomyces luteus strain TRM45540 revealed an ANI value of 91.22%, and dDDH value of 44.00% were calculated for Streptomyces sp. VITGV156 with Streptomyces luteus strain TRM45540 (Accession ID – PRJNA248298; Taxonomic ID − 67332) as shown in Table 1. This reveals that VITGV156 is a distinctively new species. High ANI value (above 95%) and high DDH estimations (Formula 2 above 70%) were usually observed for bacterial species differentiation previously (Yoon et al. 2017). Therefore, both strains are closely related, but both are not belonging to the same species. The results show as Streptomyces sp. VITGV156 could be a new species of the genus Streptomyces.
A total of 6,259 protein coding genes were identified (Table 1) and 151 genes out of them showed no resemblance to the existing genes which could be due to the presence of new metabolic pathways. Similar report previously recorded in Streptomyces sp. RLA2-12 showed 157 genes showed potential property in involved in the metabolic pathway by Nicault et al. (2020). Previous reports from the endophytic Streptomyces sp. obtained from tomato plant showed a significant antibacterial (Shah et al. 2017), antifungal, activity, enhance disease resistance (Abbasi et al. 2019) and plant growth promotion (Zarandi et al. 2021).
Out of the total genes, a total of 406 genes were involved in metabolism of cofactors, vitamins, terpenoids, polyketides and other secondary metabolites (Table 2). Moreover, the previous study by Zhang et al. (2019) reports the similar scenario in Streptomyces sp. CC0208 contains 439 genes which involved in the metabolism of cofactors, vitamins, terpenoids, glycan, polyketides and other secondary metabolites.
Table 2
Genes associated with secondary metabolites
Pathways | Streptomyces sp. VITGV156 |
Metabolism of cofactors and vitamins | 184 |
Metabolism of terpenoids and polyketides | 72 |
Xenobiotics biodegradation and metabolism | 70 |
Biosynthesis of other secondary metabolites | 80 |
The genome was further analysed for the presence of BGCs using antiSMASH 6.0 (Medema et al. 2011). A total of 29 putative secondary metabolites were predicted by antiSMASH 6.0 (Table 3). Sivakala et al. (2021) reported 36 well-defined BGCs from Streptomyces sp. SAJ using antiSMASH.
Table 3
Secondary metabolite Biosynthetic Gene Cluster of Streptomyces sp. VITGV156 using antiSMASH 6.0
Region | Type | Most similar known cluster | Similarity |
Region 2.1 | Indole | 5-isoprenylindole-3-carboxylate β-D-Glycosyl ester | 23% |
Region 2.2 | Terpene | Isorenieratene | 63% |
Region 3.1 | NRPS-like | Streptothricin | 95% |
Region 3.2 | T3PKS | Herboxidiene | 8% |
Region 7.1 | Ectoine | Ectoine | 100% |
Region 7.2 | Melanin | Melanin | 60% |
Region 7.3 | Siderophore | Desferrioxamin B / Desferrioxamine E | 83% |
Region 10.1 | NRPS-like | - | - |
Region 10.2 | PKS-like, furan, Lanthipeptide-class-V | Methylenomycin A | 9% |
Region 11.1 | Lanthipeptide-class-III | Catenulipeptin | 60% |
Region 12.1 | Terpene | Albaflavenone | 100% |
Region 12.2 | T2PKS | Spore Pigment | 66% |
Region 13.1 | T2PKS, PKS-like | Fluostatins M-Q | 67% |
Region 15.1 | Butyrolactone | Prejadomycin / Rabelomycin / Gaudimycin C / Gaudimycin D / Uwm6 / Gaudimycin A | 6% |
Region 16.1 | Siderophore | - | - |
Region 17.1 | RiPP-like | - | - |
Region 17.2 | Terpene | Geosmin | 100% |
Region 17.3 | Siderophore | Paulomycin | 9% |
Region 18.1 | NRPS | CDA1b / CDA2a / CDA2b / CDA3a / CDA3b / CDA4a / CDA4b | 72% |
Region 18.2 | Terpene | Hopene | 100% |
Region 18.3 | T1PKS | Vicenistatin | 60% |
Region 19.1 | T1PKS | Sipanmycin | 13% |
Region 20.1 | T1PKS | Nystatin A1 | 27% |
Region 21.1 | T1PKS | Streptovaricin | 29% |
Region 21.2 | Terpene | Versipelostatin | 5% |
Region 21.3 | RiPP-like | Informatipeptin | 42% |
Region 21.4 | NRPS | Coelichelin | 100% |
Region 21.5 | NRPS, lanthipeptide-class-i | Coelibactin | 90% |
Region 21.6 | Lanthipeptide-class-iii | SapB | 100% |
NRPS - non – ribosomal peptide synthetase |
T1PKS – Type 1 Polyketide Synthases |
T2PKS – Type 2 Polyketide Synthases |
T3PKS – Type 3 Polyketide Synthases |
RiPP - Ribosomally synthesized and post-translationally modified peptides |
The Table 3 also shows some rare antibiotics such as coelichelin, fluostatins, vicenistatin, nystatin, sipanmycin, and informatipeptin. These antibiotics were previously reported in several strains such as coelichelin – Streptomyces sp. ICC1 (Gosse et al. 2019), fluostatins – Streptomyces sp. PKU-MA00045 (Jin et al. 2018), vicenistatin - Streptomyces sp. SD85 (Low et al. 2018), nystatin – Streptomyces youssoufiensis OUC6819 (Yao et al. 2018), sipanmycin – Streptomyces sp. strain CS149 (Malmierca et al. 2018), and informatipeptin – Streptomyces sp. VN1 (Nguyen et al. 2020).
Table 3 show how this species is unique with many biosynthetic gene clusters, having more possibility for novel compounds belonging to different clusters such as terpene (versipelostatin 5%), butyrolactone (prejadomycin 6%), T3PKS herboxidiene 8%), Siderophore (paulomycin 9%), PKS Lanthipeptide-class-V (methylenomycin A 9%) and T1PKS (sipanmycin 13%). As the compounds are having very low similarity (5 to 13%) they could be new derivatives of existing compounds.
BGCs are including an unidentified non ribosomally synthetases, and a ribosomally synthesized and post-translationally modified peptides and a siderophore compound. Also, three compounds show relatively less similarity (less than 20%) to the known natural products suggesting them to be unidentified compounds. Cruz-Morales et al. (2017) reported these secondary metabolites like siderophore in Streptomyces sp. CC77. Of the total 29 BGCs responsible for production of secondary metabolites, 34% (10 BGCs) corresponds to the biosynthesis of peptide compounds, 24 % (7 BGCs) corresponds to the biosynthesis of polyketides, 13% (4 BGCs) corresponds to the synthesis of terpenes and 10% (3 BGCs) corresponds to the synthesis of siderophores. Similar report was published in Streptomyces sp. which consists by Park et al. (2021) 32 biosynthetic gene cluster, Non-ribosomal peptide synthetases, siderophores, and terpenes were also present in genomes.
An indole compounds less similar to 5-isoprenylindole-3-carboxylate β-D-Glycosyl ester was produced by the strain. Indole compounds are well known for their growth promoting activity. Similarly, Goudjal et al. (2015), suggested that Siderophores associated with Streptomyces sp.TL7 is involved in promoting plant growth. Analysis of bacteriocins by BAGEL revealed the presence of antimicrobial peptide zoocin A and lanthipeptides belong to class I and IV. This same Lanthipeptides are ribosomally synthesized and post-translationally modified microbial secondary metabolites by Iftime et al. (2015) in the strain Streptomyces collinus Tü 365. These results indicate that the strain Streptomyces sp. VITGV156 is indeed a novel strain producing a rich repertoire of secondary metabolites with promising applications.