|
Paenibacillus mucilaginosus, one of the typical silicate bacteria, has long been used in agriculture, bioleaching engineering and wastewater treatment. Paenibacillus mucilaginosus KNP414, isolated from the soil of Tianmu Mountain, Zhejiang Provice (China), was proved effective in dissolution of mineral phosphate and potassium and nitrogen fixation. In order to understand the basic genetic characteristics, the genome of P. mucilaginosus KNP414 was sequenced in this study.Firstly, we sequenced the whole genome sequence of P. mucilaginosus KNP414 using a Whole Genome Shotgun (WGS) method. Three DNA libraries with insert size of 400bp, 2kb and 6kb were constructed and sequenced by the Illumina/Solexa sequencing platform. Altogether 5680318, 11019228 and 15603038 reads were obtained from the three libraries, and the genome coverage is 53.8, 96.6 and 147.7-fold, respectively. After deletion of low quality reads and duplications and correction of error reads, 5517056, 8815902 and 1177438 reads were obtained with 53.5, 61.8 and 11.1-fold genome coverage, respectively. The genome of P. mucilaginosus KNP414 was then successfully assembled using improved methods, indicating its advantage during assembly of the genome.Secondly, the basic genomic information was analyzed. The results showed that P. mucilaginosus KNP414 had a circular chromosome of 8,557,776bp and the GC content was 58.45%. The genome encoded 7,827 putative proteins, 82 tRNAs, and 13 16S-23S-5S rDNA operons. A lot of repeat sequences, including insert sequences, tandem repeat sequences and long terminal repeat, were predicted, which might be the result of adaption to new environment or the insertion and deletion of gene on a large scale. Analysis of COG showed that the genome encoded complicated signal transduction and carbohydrate metabolism network. Strain KNP414 was pridicted to use fructose, mannose, galactose, starch, sucrose, amino sugar, ribonucleotide sugar, pyruvate, glyoxylate, C5- branch dibasic acid, nositol, vitamin C and detraine. Interestly, some genes related to carbon dioxide and nitrogen fixation were first discovered.In the end, comparative genomics, such as the basic characteristics of the genome, synteny, functional classification and basic metabolism, was carried out between strain KNP414 and other three sequenced Paenibacillus strains. Category G and T of COG was found to play a vital role in the chromosome of P. mucilaginosus KNP414, which indicated vigorous metabolism of carbohydrate and signal transduction. Comparatively, strain KNP414 held varied genes special in metabolism of nitrogen, glycerophospholipid, pyruvate, glyoxylate and dicarboxylate, carbon dioxide fixation, and ABC transporter. Analysis of two-component system showed that abundant proteins of P. mucilaginosus KNP414 related to varied signal transduction, such as nitrogen assimilation, carbon storage regulator, chemotaxis family, sporulation and biofilm formation and tolerance heavy metal. These features indicated that P. mucilaginosus KNP414 may have high capacity of environmental adaptation.In conclusion, whole genome sequence of P. mucilaginosus KNP414 will provide theory basis in research and application. And multi-function mechanism studies of P. mucilaginosus KNP414 also need a long accumulation process, and some new characterics will be verified in the future.
|