| Members of the genus Pseudomonas are Gram-negative, rod-shape, and aerobic bacteria. They colonize diverse habitats because of their remarkable metabolic and physiologic versatility, and are important for industrial, agricultural and medical applications. Siderophore high-yielding Pseudomonas strain HYS was isolated from water of East Lake of Wuhan. The special siderophore secreting ability indicates that strain HYS have a special iron acquisition or regulation system, and this strain has potential in biocontrol applications. Its unknown genetic background is a barrier for molecular and the relevant bio-effects analysis of this strain. In this study, the genomic DNA of strain HYS was sequenced with Solexa paired-end sequencing technology to obtain the genetic information.Sequencing genomic DNA of Pseudomonas sp. HYS yielded519.1838Mb effective raw paired-end sequence reads. Raw paired-ended reads were de novo assembled using the SOAPdenovo alignment tool which generated231contigs excluding contigs shorter than200bp, and then assembled into64scaffolds by paired-end mapping. The total length of the draft genome is5,639,475bp. Based on the ratio of used paired-end sequence reads, draft genome data covered91.06%of the real whole genome. These sequences have been deposited at NCBI Whole Genome Shotgun database under the accession AJJP00000000. The version described in this paper is the first version AJJPO1000000.Average nucleotide identity of the draft genome with33sequenced genomes from nine Pseudomonas species were calculated by using the BLASTN algorithm, showing that the strain is closely related to strains from P. putida group, but not belongs to any of them. Three phylogenetic trees based on sequences of 'housekeeping'genes16S rRNA, gyrB and rpoD have been constructed respectively, showing that strain HYS and P. vranovesis always located in the same branch. In the tree of16S rRNA gene, this branch is located inside of the P. putida group, but it located independently outside of the P. putida group in other two trees.Analysis of isoprenoid quinines identify strain HYS has the same type of ubiquinone as members of P. putida group. The characterization of fatty acids components is different from P. putida type strain and P. vranovesis, and also the ability to hydrolyze gelatin. According to the results above, strain HYS and P. vranovesis are independently evolutional branch, whith is closely related to P. putida group. Strain HYS is either a strain of P. vranovesis with different biochemical characteristic or a new species.Comparative genomics analysis of strain HYS with plant-promotion Pseudomonas spp. reveal that:1) it has potential colonize plant rhizosphere but lacks of plant pathogenetic system;2) it may inhibit pathogenetic fungus by competitive iron absorbtion;3) it has gene clusters encoding potential nematode killing toxins. The first two hypothesises are verified by other groups of our lab, and this study focus on the nematode killing ability of the strain HYS. Model organism Caenorhabditis elegans has been chosen to perform the nematode killing assay.Strain HYS kills Caenorhabditis elegans embryo by delaying the embryogenesis and triggers autophagy of embryo cells. Half of adult worms feed on HYS died after3.6d, while the time is12.8d if feed on normal food.C. elegans has a characteristic nematode biochemistry and shares structures found to be important to parasitic species. Since, most of the plant parasitic species lay eggs in soil and get into plant after L2stage, the embryo killing ability of HYS makes it a potential biocontrol agent to kill embryo of plant parasitic nematode.By tested siderophore defective mutant of strain HYS, confirm that siderophore is not the toxin killing embryo, and find that GacS and GacA involved in killing assay. Gene knockout and rescue assay verify this nematicide activity is positively controlled by GacS/GacA two-component regulatory system and blocked by RsmA. |
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