Complete genome sequence of Streptomyces californicus ADR1, an anti-infective, anti-biofilm and anti-oxidant producing endophyte isolated from the medicinal plant Datura metel.
This high-quality genome provides crucial insights into the biosynthetic potential underlying potent antimicrobial and antioxidant activities of the strain ADR1.
Abstract
OBJECTIVE
Streptomyces californicus strain ADR1 is an endophytic actinobacterium isolated from Datura metel that produces secondary metabolites with potent antibacterial and anti-biofilm activities against WHO-listed high-priority Gram-positive pathogens. While anti-bacterial and antioxidant potential of the strain ADR1 has been extensively characterized, its complete genome sequence remains to be investigated for further insights into its biosynthetic potential. This study presents the complete genome sequence analysis of the strain ADR1 to provide a robust genomic foundation for understanding its metabolic versatility and biosynthesis of compounds with therapeutic significance.
DATA DESCRIPTION
The ADR1 genome was sequenced using Illumina HiSeq. The assembly comprised 262 scaffolds with a total genome size of 8.4 Mb and G + C content of 72.5%, containing 7427 protein-coding genes. AntiSMASH and IIT-Hyderabad novelBGC analysis revealed 39 biosynthetic gene clusters, including non-ribosomal peptide synthetases, type I polyketide synthases, terpene and melanin clusters, correlating with the diverse therapeutic compounds previously identified through GC-MS analysis. This high-quality genome provides crucial insights into the biosynthetic potential underlying potent antimicrobial and antioxidant activities of the strain ADR1.
Phylogenetic and functional genomic analyses were carried out to help explaining the endophytic lifestyle and the biocontrol activity of
Streptomyces
sp. strain DEF39, able to reduce
Fusarium graminearum
infection as well as deoxynivalenol production in wheat plants. Specifically, in this work, genes and biosynthetic pathways linked to secondary metabolite production, biocontrol activity, and plant interactions were identified. This approach supports the experimentally validated capability of DEF39 to protect plants from fungal diseases, highlighting the potential of genomics studies.
Streptomyces
sp. DEF39 was isolated as an endophyte from
Secale cereale
in Italy and has been shown to colonize wheat (
Triticum
spp.) and act as a biocontrol agent of Fusarium head blight. The complete genome (9.12 Mb) (GCA_978019405.1), assembled through a hybrid strategy based on long and short accurate reads combination, is composed of a linear chromosome of 8,887,323 bp with a GC content of 71.59% and a linear plasmid of 233,172 bp with a GC content of 69.27%. Phylogenetic analyses based on the whole genome demonstrated that DEF39 belongs to
Streptomyces anulatus
species (ANI and dDDH value of 99.13% and 92.8%, respectively with the reference genome GCA_001434355.1). Functional annotation revealed 9,556 genes (CDS). Respectively, antiSMASH and PLaBAse bioinformatic tools predicted 15 putative secondary metabolite biosynthetic gene clusters, as well as 5,203 genes putatively associated with plant growth promotion.
Irene Valenti, A. Motta, M. Saracchi et al.· BMC Genomic Data· 0 citations
The previous studies in our laboratory have shown that Bacillus velezensis strain BV2007 exhibits a significant biocontrol effect against apple tree canker. In this study, the complete genomic sequence and annotation information of the strain were obtained by using PacBio Revio platform and Illumina sequencing technologies. Sequence analysis results do not include gaps or plasmids. The final assembled genome of strain BV2007 is 3,916,866 bp in length, with an average GC content of 46.46%. It contains 4,020 predicted protein-coding genes, 87 tRNAs, 27 rRNAs, and 16 sRNAs. A total of 13 secondary metabolite biosynthetic gene clusters were identified in the genome, which may contribute significantly to the biocontrol activity of this strain. This genome sequence has provided a basis for further understanding of the biocontrol mechanism of B. velezensis strains.
Yinuo Liu, Tianhao Fu, Xiaohong Luo et al.· PhytoFrontiers™· 0 citations
Bacillus velezensis strain H166, isolated from the apple rhizosphere, exhibits strong biocontrol efficacy against apple replant disease (ARD), a complex soilborne disease in which Fusarium oxysporum can act as an important fungal pathogen. To elucidate the underlying biocontrol mechanisms, a high-quality genome assembly of strain H166 was generated using PacBio HiFi sequencing. The genome of strain H166 consists of a single circular chromosome of 3,929,791 bp with a GC content of 46.5%, and contains 4,035 protein-coding genes, 86 tRNA genes, 27 rRNA genes, and 16 sRNA genes. Twelve secondary metabolite biosynthetic gene clusters were identified, including those associated with fengycin, surfactin, and bacillaene biosynthesis. These gene clusters are presumed to be closely associated with the biocontrol functions of this strain against Apple Replant Disease. The genome sequence provides important foundational data for further elucidating the molecular mechanisms underlying the biocontrol activity of B. velezensis strain H166.
An integrated omics study provides foundational insights into the endophytic potential and genomic distinctiveness of AwOcstreb1, isolated from halophytic rice, and opens new avenues for exploring A. welwitschiae for sustainable agriculture and fungal biology.
Nishat Tamanna, Md Nafis Ul Alam, Arifa Akhter Airin et al.· Microbial Genomics· 0 citations
Findings suggest that strain D18 possesses adaptive strategies for survival in deep-sea environments and highlight its potential as a source of novel secondary metabolites.
Weifeng Liu, Conghui Huang, Aifang Deng et al.· Marine Genomics· 0 citations