Genome Sequence of Paenibacillus sp. Strain Aloe-11, an Endophytic Bacterium with Broad Antimicrobial Activity and Intestinal Colonization Ability

Abstract

Paenibacillus sp. strain Aloe-11, a Gram-positive, spore-forming, facultatively anaerobic bacterium isolated from the root of Aloe chinensis in the southwest region of China, has excellent antibiotic activity and intestine colonization ability. Here, we present the 5.8-Mb draft genome sequence of Paenibacillus sp. strain Aloe-11.

GENOME ANNOUNCEMENT

Paenibacillus, whose members once belonged to the genus Bacillus, was reclassified as a separate genus in 1993 (1). More than 120 Paenibacillus species have been isolated from a variety of habitats and widely used in areas such as agriculture, industry, medicine, and environmental remediation (11–14). Paenibacillus sp. strain Aloe-11, an endophytic bacterium isolated from the root of Aloe chinensis, has many biological functions, such as antibiotic activity against many pathogenic bacteria and fungi and the ability to enhance the immune function of animals with its polysaccharide. According to our studies with mice and chickens, Paenibacillus sp. strain Aloe-11 can colonize the intestine over 15 days after feeding of the bacteria is stopped and can significantly promote forage fiber degradation and reduce the cellulose content in feces.

Whole-genome shotgun sequencing of Paenibacillus sp. strain Aloe-11 was completed at Beijing Genomics Institute by using Solexa paired-end sequencing technology (2). A total of 10,147,096 filtered paired-end reads (∼913.2 Mb) were obtained, representing an average of 160-fold coverage of the genome. All reads were assembled into 334 contigs (>200 bp) and 52 scaffolds using SOAPdenovo version 1.04 (9). The unclosed draft genome sequence of strain Aloe-11 shows that it has a genome size of 5,812,362 bp with a GC content of 46.62% and an N₅₀ of 230,166 bp. Based on the genomic data, 5,275 protein-coding sequences (CDS) were predicted by GeneMark.hmm (3) and annotated by BLAST sequence similarity searches against the COG, KEGG, UniProt, and nr databases, and 73 tRNA genes were also identified by using tRNAScan-SE (10).

According to comparative genome analysis with other 18 sequenced Paenibacillus strains, Paenibacillus sp. strain Aloe-11 is closest to Paenibacillus polymyxa SC2, but polymyxin-synthetic genes were not detected in strain Aloe-11. Several giant nonribosomal peptide synthetase (NRPS) genes were identified in the genome of Paenibacillus sp. strain Aloe-11, which are involved in the biosynthesis of antibiotics such as fusaricidin (5) and bacitracin (8) and of other unknown products. In the genome, there is one NRPS gene cluster, a 30-kb DNA fragment, containing four genes (lchAA, lchAB, lchAC, and lchAD) involved in the biosynthesis of surface-active lipopeptides, e.g., lichenysin (7).We also found in the genome a rich set of genes encoding secreted enzymes involved in the degradation of various plant-derived polysaccharides, including cellulases, xylanases, and pectinase. The siderophore involved in Fe³⁺ ion uptake has two synthesis pathways in Paenibacillus sp. strain Aloe-11 that are dependent on NPRSs (6) and siderophore synthetases (4). Given its high strain specificity and potential applications in multiple areas, the genome sequence of Paenibacillus sp. strain Aloe-11 is important to basic and applied research, and it will also facilitate the understanding of evolutionary relationships among Paenibacillus organisms.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AGFI00000000. The version described in this paper is the first version, AGFI01000000.