Draft genome sequence of an endophytic bacterium, Paenibacillus tyrfis strain SUK123, isolated from Santiria apiculata stem.

Here we report the draft genome sequence of an endophytic Paenibacillus tyrfis strain isolated from the Universiti Kebangsaan Malaysia reserve forest, Malaysia. The genome size was approximately 8.04 Mb, and the assembly consisted of 107 scaffolds with 168 contigs, and had a G + C content of 53%. Phylogenetic analysis of strain SUK123 using the 16S rRNA gene revealed that it belonged to the family Paenibacillaceae with the highest similarity to Paenibacillus elgii SDT (99%). Whole genome comparison of SUK123 with related species using average nucleotide identity (ANI) analysis revealed a similarity of 98% to Paenibacillus tyrfis Mst1T, 94% to Paenibacillus elgii B69T, 91% to Paenibacillus ehimensis A2T, 68% to Paenibacillus polymyxa SC2T and 69% to Paenibacillus alvei DMS29T. The draft genome was deposited at the European Nucleotide Archive (PRJEB21373).

Direct link to deposited data

http://www.ebi.ac.uk/ena/data/view/PRJEB21373.

Introduction

The bacterial genus Paenibacillus has been isolated from many environments, mostly from plant organs and their surrounding soil [1]. The species of Paenibacillus was included in the genus Bacillus until 1993 when it was proposed that the member of the “16S rRNA group 3” bacilli be distinguished from it [2]. Presently, the genus Paenibacillus consists of 395 known species [3]. Most members of the genus Paenibacillus are gram variable, either aerobic or facultatively anaerobic, rod-shaped, and endospore-forming with peritrichous flagella for motility [4]. The DNA G + C content of the various species of Paenibacillus ranges between 39 and 54 mol% whilst anteiso-C15:0 is the major cellular fatty acid and meso-diaminopimelic acid is the cell wall peptidoglycan diamino acid [5]. Most members of this genus have been reported to be producers of either active antimicrobial metabolites such as lipopeptides [6], [7], plant-growth promoting hormones [8], [9], or insecticides [10].

Experimental design, materials and methods

The endophytic Paenibacillus tyrfis, strain SUK123, was isolated from the Santiria apiculata stem located at the Universiti Kebangsaan Malaysia forest reserve, whilst screening for endophytes with antimicrobial potential against ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens. After sample collection, the stem surface was sterilized to avoid surface-bound epiphytes as described previously [11]. The sterilized stem was cut into a 2 cm section and plated on water agar plate medium from where SUK123 (an antibiotic producing bacterium) was isolated.

Endophytic Paenibacillus tyrfis DNA was extracted using an Ultraclean Microbial DNA Isolation Kit as described by the manufacturer (Mo Bio Laboratories, 2746 Loker Ave W # A, Carlsbad, CA 92010, USA). The bacterium was identified by sequencing its 16S rRNA gene. Sequence was performed on Illumina Miseq platform (Majorbio, China) by 2 × 400 bp paired-end libraries. The raw sequence quality was assessed using PRINSEQ lite version 0.20.4 and the genome was assembled using SOAPdenovo v2.04 with all parameters set by default [12] and GapCloser v1.12 was used to fill local inner gaps. The open reading frames (ORFs) were predicted using Glimmer 3.02 [13]. The biological functions of these predicted ORFs were annotated using various databases.

Data description

The analyses of the assembled genome revealed a genome size of about 8,041,385 bp made of 107 scaffolds, 168 contigs, and with a G + C content of 53.06% and N50 contigs size of 197,909 (Table 1). The genome was annotated using Rapid Annotation Subsystems Technology server [14].

Table 1

Statistics of assembled sequence length.

No. of all scaffolds	107
Bases in all scaffolds	8,041,385
No. of large scaffolds (> 1000 bp)	73
Bases in large scaffolds	8,024,609
Largest length	505,699
Scaffold N50	257,089
Scaffold N90	62,404
G + C content (%)	53.061
No. of all contigs	168
Bases in all contigs	8,041,324
No. of large contigs (> 1000 bp)	114
Bases in large contigs	8,013,898
Largest length	501,150
Contig N50	197,909
Contig N90	48,401

The RAST server prediction revealed 7368 coding sequences (CDS) with a total of 2880 CDS (40%) constituting 2747 and 133 of non-hypothetical and hypothetical proteins respectively in the subsystem coverage. A total of 4488 CDS (60%) comprising 2003 and 2485 of non-hypothetical and hypothetical proteins respectively were outside the subsystem coverage (Fig. 1).

Fig. 1

A diagrammatic representation of Paenibacillus tyrfis strain genome subsystem coverage as annotated by RAST.

The average nucleotide identity (ANI) [15] analysis of SUK123 with closely related species, revealed a similarity index with Paenibacillus tyrfis Mst1T (98.06%), Paenibacillus elgii B69T (93.98%), Paenibacillus ehimensis A2T (91.17%), Paenibacillus alvei DMS29T (68.81%) and Paenibacillus polymyxa SC2T (68.27%), suggesting our isolate most closely related to Paenibacillus tyrfis Mst1T.

Declaration of interest

We declare no conflict of interest with respect to this article titled ‘Draft genome sequence of an endophytic ’ submitted to Genomics data journal.

Specifications
Organism/cell line/tissue	Paenibacillus tyrfis
Sex	Not applicable
Sequencer or array type	Illumina Miseq
Data format	Raw data and analyzed i.e. assembled
Experimental factors	Paenibacillus tyrfis strain was isolated from Santiria apiculata stem
Experimental features	Isolation of bacteria, Genome sequencing, de novo assembly
Consent	Not applicable
Sample source location	Universiti Kebangsaan Malaysia reserve forest, Latitude & Longitude – 2.9125 & 101.7872