Draft Genome Sequence of Paenibacillus elgiiB69, a Strain with Broad Antimicrobial Activity

Abstract

Here, we report the draft genome sequence of Paenibacillus elgiiB69, which was isolated from soil and has broad-spectrum antimicrobial activity. As far as we know, the P. elgiigenome is the largest of the Paenibacillusgenus for which genome sequences are available. Multiple sets of genes related to antibiotic biosynthetic pathways have been found in the genome.

GENOME ANNOUNCEMENT

Recently, interest in the Paenibacillusgenus has been rapidly growing, for many Paenibacillusspecies have been shown to produce various enzymes and antimicrobial substances, such as xylanase and polymyxins (3, 7). There are more than 110 species that have been discovered in this genus (8). The Paenibacillus elgiistrain B69 was isolated from soil samples collected from Tianmu Mountain in Hangzhou, China, and displays significant activity against all tested microorganisms (9).

Whole-genome shotgun (WGS) sequencing of Paenibacillus elgiiB69 was performed with Solexa paired-end sequencing technology (1). A total of 2,564.46 million base pairs of reads were generated to reach a depth of ∼322-fold genome coverage and were assembled into 278 contigs using SOAPdenovo version 1.04 (4). Furthermore, the paired-end information was used to join contigs into 184 scaffolds (>1 kb in size). The open reading frames were annotated by using Glimmer version 3.0 (2) and by searching against the COG, KEGG, UniProt, and nr databases.

The unclosed draft genome sequence of Paenibacillus elgiiB69 showed a genome size of 7,981,270 bp (scaffold length) with a mean GC content of 52.57%. There are 7,907 coding sequences (CDSs), and 51 tRNAs were identified by tRNAscan-SE (5). In addition, 330 insertion sequence elements, 330 transposases, and 227 tandem repeats were found.

Gene family analysis of Paenibacillus elgiiB69 and Paenibacillussp. strain JDR-2 showed that 123 gene families were constructed (more than 10 genes for each of them), and the largest gene family included 414 genes (186 from JDR-2). From the 7,907 identified genes, 5,704 CDSs were classified into 22 functional COG groups, and the unannotated genes may be assigned upon closure of the genome. One of the notable features of B69 is its potential to produce secondary metabolites, such as pelgipeptins (9) and paenibactin, which is a novel catecholic siderophore identified recently in our lab (unpublished data). No polymyxin synthetase gene was found, but several unknown giant gene clusters were found in the B69 genome, including the genes for one polyketide synthetase (PKS), two nonribosomal peptide synthetases (NRPS), three hybrid NRPS-PKS synthetases, and a lantibiotic-synthetic gene cluster. Surprisingly, the genome size of P. elgiiis larger than that of other Paenibacillusspecies with genome sequences available (3, 6), such as P. polymyxa(∼5.7 Mb), suggesting that the size difference could have arisen through acquisition of more genes by gene duplication or horizontal transfer during evolution. Comparative genome analysis of Paenibacillusstrains will help us identify diverse antibiotic biosynthetic genes and elucidate the evolution of biosynthetic pathways among the members of this genus.

Nucleotide sequence accession number.

The sequence from this whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession number AFHW00000000. The version described in this paper is the first version, AFHW01000000.