Draft Genome Sequence of Paenibacillus peoriae Strain KCTC 3763^T

Abstract

Paenibacillus peoriae is a potentially plant-beneficial soil bacterium and is a close relative to Paenibacillus polymyxa, the type species of the genus Paenibacillus. Herein, we present the 5.77-Mb draft genome sequence of the P. peoriae type strain with the aim of providing insight into the genomic basis of plant growth-promoting Paenibacillus species.

GENOME ANNOUNCEMENT

Despite its general phenotypic homogeneity, Paenibacillus polymyxa, a well-known plant growth-promoting rhizobacterium (7) that was formerly classified as Bacillus polymyxa (2), exhibits both variable characteristics and genetic diversity. The latter findings have led to the proposal of a new species that formerly belonged to P. polymyxa. Bacillus peoriae, isolated from soil, was originally recognized as a new species from gas-producing Bacillus polymyxa on the basis of DNA relatedness, multilocus enzyme electrophoresis analysis, and other phenotypic characteristics (8). It was later reclassified as Paenibacillus peoriae with an emended description of the species (4).

The role of P. peoriae isolates in the rhizosphere remained unexplored until very recently. With the exception of antimicrobial activity against plant pathogens (10) and the production of hydrolytic enzymes that may be beneficial to crop plants (1), there are few reports regarding the utility of P. peoriae. While analyzing the genome sequence of P. polymyxa E681, a potent plant growth-promoting strain isolated from the rhizosphere of barley (5), we found that the 16S rRNA gene sequence is much closer to that of P. peoriae. This led us to determine the genome sequence of P. peoriae type strain KCTC 3763^T (ATCC 51925^T) for deciphering the genomic basis to understand the genus Paenibacillus as a ubiquitous soil inhabitant of potential agricultural and ecological interest.

Over 6.1 Gb of Illumina GA IIx paired-end reads (121-nucleotide cycle) were de novo assembled using CLC Genomics Workbench version 4.7.2 (CLC bio). The resulting assembly consists of 53 contigs of over 200 bp (N₅₀, 276,721 bp; maximum contig size, 902,703 bp; 46.4% GC) totaling 5.77 Mb. Using the same data set, Velvet (11) version 1.1.05 with a k-mer size of 61 produced an assembly consisting of 86 scaffolds totaling 5.75 Mb (N₅₀, 219,429 bp; maximum contig size, 662,979 bp). When the largest contigs produced by each assembler were compared using MUMmer (6), 99.7% of the sequences matched with a percent identity of 99.995% over 900,187 bp of total alignment blocks, which implies consistent results regardless of the assembler program. A partial finishing was carried out to confirm the presence of a putative plasmid (31,474 bp) and to join four contigs encoding a nonribosomal peptide synthetase (NRPS) gene for the biosynthesis of a novel heptapeptide antibiotic.

Automatic genome annotation using the RAST server (3), based on the CLC Genomics Workbench-derived contigs, gave a 39% subsystem coverage for 5,251 putative coding sequences. An analysis of the average nucleotide identity (9) across complete genome sequences of P. polymyxa strains (E681 and SC2) and draft sequences of P. polymyxa ATCC 842^T and P. peoriae KCTC 3763^T revealed that P. peoriae KCTC 3763^T is closer to E681. In the draft sequences, we were able to identify gene clusters for the biosynthesis of tridecaptin and a novel heptapeptide antibiotic that is similar to hexapeptide fusaricidin antibiotics, along with several contigs harboring NRPS genes encoding unknown products. We were also able to determine several genes for extracellular carbohydrases, including an amylase, a xylanase, a cellulase, and several glucanases, which may be responsible for the utilization of plant-derived polysaccharides in the rhizosphere.

Nucleotide sequence accession numbers.

The draft genome sequence was deposited in GenBank under accession number AGFX00000000. The version described in this paper is the first version, AGFX01000000.