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The complete genome sequence of Hafnia alvei A23BA: a potential antibiotic-producing rhizobacterium. [Dataset]

Contributors

Opeyemi K. Awolope
Data Collector

Noelle H. O'Driscoll
Data Collector

Alberto Di Salvo
Data Collector

Andrew J. Lamb
Data Collector

Abstract

Objectives: The urgent need for novel antibiotics cannot be overemphasized. Hafnia alvei A23BA was isolated from plant rhizosphere as part of an effort to recover novel antibiotic-producing bacterial strains from soil samples. The genome of the isolate was sequenced to facilitate mining for potential antibiotic-encoding biosynthetic gene clusters and to gain insights into how these gene clusters could be activated. Data description: Here, we report the complete genome sequence of H. alvei A23BA obtained from the hybrid assembly of Illumina HiSeq and GridION reads. The genome, consisting of a circular chromosome and a circular plasmid, is 4.77 Mb in size with a GC content of 48.77%. The assembly is 99.5% complete with genomic features including 4,217 CDSs, 125 RNAs, and 30 pseudogenes. Thiopeptide, beta-lactone, siderophore, and homoserine lactone biosynthetic gene clusters were also identified. Other gene clusters of interest include those associated with bioremediation, biocontrol, and plant growth promotion- all of which are reported for H. alvei for the first time. This dataset serves to expedite the exploration of the biosynthetic and metabolic potentials of the species. Furthermore, being the first published genome sequence of a soil isolate, this dataset enriches the comparative genomics study of H. alvei strains.

Citation

AWOLOPE, O.K., O'DRISCOLL, N.H., DI SALVO, A. and LAMB, A.J. 2021. The complete genome sequence of Hafnia alvei A23BA: a potential antibiotic-producing rhizobacterium. [Dataset]. BMC research notes [online], 14, article number 8. Available from: https://doi.org/10.1186/s13104-020-05418-2

Acceptance Date Dec 9, 2020
Online Publication Date Jan 6, 2021
Publication Date Dec 31, 2021
Deposit Date Jan 21, 2021
Publicly Available Date Jan 29, 2021
Publisher Springer Verlag
DOI https://doi.org/10.1186/s13104-020-05418-2
Keywords Hafnia alvei; H. alvei; Genome mining; Biosynthetic gene clusters; Antibiotics; Rhizobacteria; Bioremediation; Biocontrol; Plant growth-promoting rhizobacteria
Public URL https://rgu-repository.worktribe.com/output/1085361
Type of Data 5 PDF files, 3 JPEG files, 1 Fastq file, 1 Fasta file and supporting text file.
Collection Date Nov 30, 2020
Collection Method H. alvei A23BA was recovered from the rhizosphere of a garden plant in Aberdeen, Scotland (57.101 N 2.078 W). It was isolated using an ultra-minimal substrate medium (Data file 1) [9]. Upon isolation and strain purification, isolate was cultivated in nutrient broth (Oxoid, UK) at 37 °C for 24 h. Overnight culture was centrifuged and gDNA was extracted from pellets with the DNeasy® Ultraclean® Microbial Kit for DNA Isolation (Qiagen, UK). Isolate was preliminarily identified by 16S rRNA gene sequence comparison as H. alvei with 99% identity score. Libraries were subsequently prepared from extracted gDNA by MicrobesNG (Birmingham, UK) for whole genome sequencing. For Illumina sequencing, libraries were prepared using the Nextera XT Library Prep Kit (Illumina, USA) and sequenced with the Illumina HiSeq system using a 250 bp paired end protocol. For GridION (Oxford nanopore) sequencing, libraries were prepared with Oxford nanopore SQK-RBK004 kit and/or SQK-LSK109 kit with Native Barcoding EXP-NBD104/114 (ONT, UK) using 400-500 ng HMW DNA. Sequencing was performed on a FLO-MIN106 (R.9.4 or R.9.4.1) flow cell in a GridION (ONT, UK). Illumina sequencing run produced 4,973,530 short reads that were trimmed and paired using Trimmomatic [10] v0.30 with a sliding window quality cut-off of Q15. Ninety eight percent of reads were retained, and quality was assessed with FastQC [11] v0.11.8. Mean phred score across each base position was assessed with MultiQC [12] and found to be ≥ 28 (Data file 2) [13]. GridION sequencing run produced 18,642 reads with the mean read quality score of 10.5 (data file 3) [14] as assessed with NanoStat [15]. Paired short reads and long reads from GridION sequencing were assembled with Unicycler [16] v0.4.8.0. Assembly quality was assessed with QUAST [17] v5.0.2- two contigs (one chromosome and one plasmid) were identified with a total length of 4,772,047 bp, N50 value of 4,687,005 bp and #N’s per 100 kbp value of 0 (data file 4) [18]. Assembly completeness was assessed with BUSCO [19] v3.0.2 and found to be 99.5% (data file 5) [20]. Identity was confirmed as H. alvei by ANI analysis using the FastANI tool [21], with the ANI value of 97.8167. Gene and functional annotations were performed with PGAP [22] v4.11 and RASTtk [23]; pathways analyses were performed using the KEGG database [24] Rel 93.0 and the eggNOG mapper [25] vs 2.0.0. smBGCs were identified with antiSMASH [26] v5.0. Genome map was drawn with CGView [27] and presented in data file 6 [28]. In summary, the complete genome sequence of H. alvei A23BA is 4,772,047 bp in size with the overall GC content of 48.77% and sequencing coverage of 256.0 x. It comprises of one circular chromosome (4,687,005 bp; GC content 48.8%) and one circular plasmid (85,042 bp; GC content 47.2%). Genomic features include 4,217 CDSs, 25 rRNA, 92 tRNA, 8 ncRNA, 30 pseudogenes and 2 CRISPRs. Thiopeptide, beta-lactone (both showing little or no homology to known smBGCs) and siderophore smBGCs were identified (data file 7) [29]. Thiopeptides and beta-lactones are known for their antibiotic and/or anticancer activities [30, 31], while siderophores are used clinically as “Trojan horse” to deliver antibiotics to antibiotic resistant bacteria [32]. Gene clusters commonly associated with bioremediation, biocontrol, environmental adaptation, and plant growth promotion were also identified (data file 8) [33]. Please see Table 1 for links to data files 1–8. Given the quality control measures applied and results of analyses undertaken, we believe Hafnia alvei strain A23BA chromosome, complete genome [34] represents a high-quality dataset that would expedite the exploration of the biosynthetic and metabolic potentials of H. alvei A23BA and would also enrich the comparative genomics study of H. alvei strains.