Abstract
Paenibacillus polymyxa SC2 is an important plant growth-promoting rhizobacterium (PGPR). Here, we report the complete genome sequence of P. polymyxa SC2. Multiple sets of functional genes have been found in the genome. As far as we know, this is the first complete genome sequence of Paenibacillus polymyxa.
Paenibacillus polymyxa (formerly Bacillus polymyxa) (2), the type species of Paenibacillus, is considered a plant growth-promoting rhizobacterium (PGPR) (12). P. polymyxa is widespread in the soil and widely used in agriculture, industry, and environmental remediation because of its multiple functions (10). P. polymyxa strain SC2 was isolated from the rhizosphere of pepper in Guizhou, China (15), and has been widely used in biological control of soil-borne plant diseases.
Whole-genome sequencing of SC2 was performed with a combined strategy of Roche/454 sequencing (9) and Solexa paired-end sequencing technology (3). Genomic libraries containing 8-kb inserts were constructed, and 153,770 paired-end reads and 103,401 single-end reads were generated using the GS FLX system, giving 15.3-fold coverage of the genome. A total of 97.42% of the reads were assembled into 25 large scaffolds, including 218 nonredundant contigs, using 454 Newbler (454 Life Sciences, Branford, CT). A total of 34,770,992 reads (3-kb library) were generated to reach a depth of 418-fold coverage with an Illumina Solexa Genome Analyzer IIx and mapped to the scaffolds using the Burrows-Wheeler Alignment (BWA) tool (8). Most of the gaps within the scaffolds were filled by local assembly of 454 and Solexa reads. The remainder and the gaps between scaffolds were filled by sequencing PCR products using an ABI 3730 capillary sequencer. The analysis of the genome was performed as described previously (6, 14).
The complete genome sequence of SC2 is composed of a circular 5,731,816-bp chromosome and a 510,115-bp plasmid, with mean GC contents of 54.58% and 37.61%, respectively. There are 5,454 coding genes, 14 rRNA operons, and 110 tRNAs in the chromosome, as well as 649 coding genes and 47 tRNAs in the plasmid. There are many essential genes in the plasmid, such as the genes involving the metabolism of purine, pyrimidine, and lipid, as well as ribosomal proteins, translation elongation factors, and different types of DNA methyltransferase, indicating its importance to the strain's life.
In comparison to Paenibacillus sp. strain JDR-2, an aggressively xylanolytic strain whose public genome is the most highly related to that of SC2, there are 2,615 shared genes and 2,645 unique genes in the chromosome of SC2. There are many genes involved in antibiotic biosynthesis in the chromosome, such as a fusaricidin-synthetic gene (PPSC2_c0086), a polymyxin-synthetic gene cluster (PPSC2_c4710-c4715), a bacitracin synthetase 1 gene (PPSC2_c2653), an iturin A synthetase gene (PPSC2_c2652), a lantibiotic-synthetic gene cluster (PPSC2_c1561-c1567), a bacillorin synthetase B gene (PPSC2_c2638), and a polyketide-synthetic gene cluster (PPSC2_c3386-c3400), according to similarities to the published gene clusters (1, 4, 5, 7, 11, 13).
Nucleotide sequence accession numbers.
The Paenibacillus polymyxa SC2 chromosome and plasmid sequences have been deposited in GenBank under accession numbers CP002213 and CP002214.
Acknowledgments
We thank Tianjin Biochip Corporation for assistance with sequencing and analysis. We thank all teachers for their contributions to the accomplishment of this task.
This work was supported by a National 863 Program of China grant (number 2010AA10A203), the Basic Scientific and Business Fund and Central Public Research Project (grant number 2010-34), and the Special Fund for the Establishment of Modern Agricultural R&D Systems (grant number nycytx-004), Ministry of Finance and Ministry of Agriculture, China.
Footnotes
Published ahead of print on 29 October 2010.
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