Genome Sequencing Of The Paenibacillus Sp.Aloe-11and Comparison With Its Closely Related Bacteria

Paenibacillus sp. Aloe-11is a nitrogen-fixation endophytic bacterium, which was isolated from the root of Aloe chinensis in our lab. This bacterium is important in agriculture, industry, medicine, and environmental remediation, because it can produce broad-spectrum antibiotics suppress many pathogenic bacteria and fungi, to secrete a variety of hydrolytic enzymes, and to produce the biosurfactant.Whole-genome shotgun sequencing of Paenibacillus sp. Strain Aloe-11was completed at Beijing Genomics Institute using Solexa paired-end sequencing technology. A total of10,147,096filtered paired-end reads (913.2Mb) were obtained, representing an average of165-fold coverage of the genome. All reads were assembled into52scaffolds using SOAPdenovo and additional PCR was conducted to curate the genome. The draft genome sequence of strain Aloe-11shows that it has a genome size of5,812,362bp with a GC content of46.62%. Based on the genomic data,5,275coding sequences (CDS) were predicted by GeneMark and annotated by BLAST sequence similarity searches against the COG, KEGG, UniProt, and nr databases,73tRNA genes were identified by using tRNAScan-SE and12rRNA were identified by rnammer and BLASTN similarity search. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AGFI00000000.Among the5,275CDS, numerous nonribosomal peptide synthetases were found in the genome of Paenibacillus sp. Strain Aloe-11. They are speculated to code Fusaricidin, Iturin, Gramicidin S, bacitracin and other antimicrobial peptides, illustrating that Paenibacillus sp. Aloe-11can produce a broad spectrum of antibacterial activity substance. A nonribosomal peptide synthetases genes cluster lchABCD was found to relate to the production of lichenysin, and this biosurfactant can increase bacterial movement ability by reducing the surface tension. There are two pathways producing siderophores in the genomes, which can increase bacterial adaptability and infection ability in environment. Nitrogenase enzyme gene cluster nifBHDKENX was also found in the Paenibacillus sp. Aloe-11genome. It is the first sequenced genome of nitrogen fixing paenibacillus. The genome contained a large number of tranportor proteins, including carbohydrate, mineral, amino acid, C4-dicarboxylate widely existed in the rhizosphere or cells of plants, which can exchange various substances between cell and environment. The functional and metabolic analysis of whole genome predicted that Paenibacillus sp. Aloe-11has metabolism system adapted to the soil and colonization of plant.Comparative genomics analysis revealed that it is different in various degrees between Paenibacillus sp. Aloe-11and other relatives. Paenibacillus sp. Aloe-11shares more common genes with Paenibacillus terrae HPL.003, followed by Paenibacillus polymyxa. Compared with other types of Paenibacillus genomes, it is greatly different in the gene structure and function, which reflects the diversity of the genus Paenibacillus.