JIA-2019-11

2669 MENG Di et al. Journal of Integrative Agriculture 2019, 18(11): 2668–2672 Pseudomonas sp. (Rani and Juwarkar 2012; Wang et al. 2014; Jariyal et al. 2015), Stenotrophomonas sp. G1 (Deng et al. 2015), and Bacillus sp. (Li et al. 2008; Ahmad et al. 2012; Jabeen et al. 2015; Ferreira et al. 2016). Among them, the genus Bacillus , as a kind of Gram-positive soil bacterium, is capable of promoting plant growth and giving protection by producing hormones, antimicrobial compounds and some volatiles (Ryu et al. 2003; Compant et al. 2005; Idris et al. 2007). Considering these useful characteristics, Bacillus members are the better choice for environmental bioremediation. Previously, Bacillus amyloliquefaciens YP6 was isolated from the rhizosphere of Lolium perenne L. on a rock phosphorus mine in Guizhou, China. This strain has confirmed to have the capacity of solubilizing phosphorus, producing indole-3-acetic acid (IAA) and siderophores (Appendix A). It also possessed excellent degradation performance, especially a wide range of OPs (Appendix A). Most of researches focused on the antimicrobial compounds and metabolomics of the genus Bacillus , some studies about the degradation of OPs by Bacillus members, which only tested one of OPs (Lakshmi et al. 2008; Ahmad et al. 2012; El-Helow et al. 2013), but few focused on degrading many OPs. As B . amyloliquefaciens YP6 had both plant growth-promoting capacity and broad-spectrum OPs removal, we reported its complete genome sequence and compared the genomes of other B . amyloliquefaciens species, which could provide genetic information for OPs metabolism and hint at the potential application of this strain in bioremediation processes. 2. Materials and methods The complete genome of B . amyloliquefaciens YP6 has been deposited at GenBank under the accession number CP032146. The BioProject, BioSample and GenBank assembly accession number for this project is PRJNA488691, SAMN09939790 and GCA_003868675.1, respectively. This strain has been deposited in China Center for Type Culture Collection (deposit ID: CCTCC; No.: M 2018875). Genomic DNA from B . amyloliquefaciens YP6 was extracted and purified using the ChargeSwitch ® gDNA Mini Bacteria Kit (Life Technologies, USA). The quantity and quality control was performed by TBS-380 Fluorometer (Turner BioSystems Inc., Sunnyvale, CA). A combination of PacBio RS and Illumina sequencing platform was used to sequence B . amyloliquefaciens YP6 genome. Using PacBio reads and Illumina reads, a circular genome sequence with no gap existed was finally assembled (Koren et al. 2012; Chin et al. 2013). NCBI Prokaryotic GenomeAnnotation Pipeline was used to annotate the genome. 3. Results and discussion The B . amyloliquefaciens YP6 genome had a chromosome with no plasmid. The total size of the genome was 4009619 bp with a G+C content of 45.9%. Gene prediction indicated a total gene length of 3554613 bp, with aGCcontent of 46.72% in the gene region and 39.66% in intergenetic region. The gene length/genome ratio was 88.65% and intergenetic region length/genome ratio was 11.35%. A total of 4 322 genes were detected from the genome sequence. The number of protein-coding genes was 4210 and RNAs was 112, containing 27 rRNAgenes and 85 tRNA genes, respectively. Although B . amyloliquefaciens YP6 was identified as a strain of B . amyloliquefaciens , it showed different genomic features compared to the other published B . amyloliquefaciens strain. According to the summary of 27 B . amyloliquefaciens complete genomes deposited in NCBI database (Table 1), the median length was 3 976 008 bp, the median of coding genes was 3 805, and the median of GC contents was 46.3%. An interesting point was that B . amyloliquefaciens YP6 had larger genome size and the most protein-coding genes. According to the isolate resources of these strains, only B . amyloliquefaciens YP6 was isolated from the rhizosphere of Lolium perenne L. on a rock phosphorus mine, the living conditions of which were worse than others. These findings were in agreement with that of Ranea et al. (2004) who reported that the genome size of microorganisms influenced their extensive adaptabilities to the environment, and under most conditions, strains with larger genome size generally might be more adaptive to complex habitats, as these microorganisms might encode more products for metabolism and stress tolerance. The functional classification based on cluster of orthologs groups (COG) assigned 3 035 protein-coding genes in different COG functional groups. When the multiple- assigned codes were included, the number of COG codes was 3083. The percentage of “function unknown (S)” was 25.3%. From the comparison of functional categories against the 9 B . amyloliquefaciens group genomes chosen based on the phylogenetic analysis of complete genome sequences (Appendix B), B . amyloliquefaciens YP6 had fewer functional genes than the other genomes for the four categories of “cell envelope biogenesis, outer membrane (M),” “translation, ribosomal structure and biogenesis (J),” “transcription (K),” and “signal transduction mechanisms (T)” (Fig. 1). B . amyloliquefaciens YP6 was living in rhizosphere of Lolium perenne L. on a rock phosphorus mine, the ionic concentration of which was very high. The reduction of M was equivalent to decreasing permeability of the cell