Abstract
The diazotrophic Burkholderia anthina MYSP113 is a vital plant growth-promoting bacteria and sugarcane root association. The present study based on a detailed analysis of sugarcane root transcriptome by using the HiSeq-Illumina platform in response to the strain MYSP113. The bacterium was initially isolated from the rhizosphere of sugarcane. To better understand biological, cellular, and molecular mechanisms, a de novo transcriptomic assembly of sugarcane root was performed. HiSeq-Illumina platformwas employed for the sequencing of an overall of 16 libraries at a 2×100 bp configuration. Differentially expressed genes (DEGs) analysis identified altered gene expression in 370 genes (total of 199 up-regulated genes and 171 down-regulated genes). Deciphering the huge datasets, concerning the functioning and production of biological systems, a high throughput genome sequencing analysis was attempted with Gene ontology functional analyses and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The report revealed a total of 148930 unigenes. 70414 (47.28%) of them were annotated successfully to Gene Ontology (GO) terms. 774 at 45 days, 4985 of 30 days and 15 days of 6846 terms were significantly regulated. GO analysis revealed that many genes involved in the metabolic, oxidation-reduction process and biological regulatory processes in response to strain MYSP113 and significantly enriched as compare to the control. Moreover, KEGG enriched results show that differentially expressed genes were classified into different pathway categories involved in various processes, such as nitrogen metabolism, plant hormone signal transduction, etc. The sample correlation analyses could help examine the similarity at the gene expression level. The reliability of the observed differential gene expression patterns was validated with quantitative real-time PCR (qRT-PCR). Additionally, plant enzymes activities such as peroxidase and superoxide dismutase were significantly increased in plant roots after the inoculation of strain MYSP113. The results of the research may help in understanding the plant growth-promoting rhizobacteria and plant interaction.
Highlights
Sugarcane crop of the family Poaceae globally fulfills the need for sugar, bioethanol, animal feed, and molasses [1,2,3]
Differential gene expression analysis identified altered gene expression in 370 genes (Fig 2) in 3 distinct groups of sugarcane root samples inoculated with strain MYSP113
The results of the study contribute significantly to a better understanding of the molecular, biological and cellular mechanisms triggered in sugarcane root by Burkholderia anthina MYSP113
Summary
Sugarcane crop of the family Poaceae globally fulfills the need for sugar, bioethanol, animal feed, and molasses [1,2,3]. Sugarcane cultivation requires a large amount of nitrogen (N) fertilizers that varies nearly 120 to 320 kg ha-1 or more. Though synthetic nitrogen is employed in the cultivation of sugarcane, only a small amount of nitrogen is taken by sugarcane, and the remaining may lead to soil and water pollution. Microbes through biological nitrogen fixation can overcome the problem of synthetic nitrogen [4]. Diazotrophic microbes that can grow under nitrogen limiting condition and fix the gaseous nitrogen to available for a plant that could be the best alternative for this problem [5, 6]. The microbes that are located in the rhizosphere are termed rhizobacteria or plant growth-promoting rhizobacteria (PGPR). There is a specific relationship between rhizosphere bacteria and sugarcane
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