Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China.
Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, Guangxi, China.
PLoS One. 2020 Apr 8;15(4):e0231206. doi: 10.1371/journal.pone.0231206. eCollection 2020.
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.
固氮伯克霍尔德氏菌 MYSP113 是一种重要的植物促生菌，与甘蔗根共生。本研究基于 HiSeq-Illumina 平台对甘蔗根转录组进行详细分析，以响应菌株 MYSP113。该细菌最初是从甘蔗根际中分离出来的。为了更好地理解生物、细胞和分子机制，对甘蔗根进行了从头转录组组装。采用 HiSeq-Illumina 平台对总共 16 个文库进行测序，配置为 2×100bp。差异表达基因（DEGs）分析鉴定了 370 个基因的表达变化（共 199 个上调基因和 171 个下调基因）。为了破译与生物系统的功能和产物有关的大量数据集，尝试进行了高通量基因组测序分析，并进行了基因本体（GO）功能分析和京都基因与基因组百科全书（KEGG）途径分析。报告共揭示了 148930 个 unigenes。其中 70414 个（47.28%）成功注释到 GO 术语。在 45 天、30 天和 15 天分别有 774、4985 和 15 个术语被显著调控。GO 分析表明，许多参与代谢、氧化还原过程和生物调节过程的基因在响应菌株 MYSP113 时发生了变化，与对照相比明显富集。此外，KEGG 富集结果表明，差异表达基因被分类到不同的通路类别中，涉及各种过程，如氮代谢、植物激素信号转导等。样品相关性分析有助于检查基因表达水平的相似性。利用定量实时 PCR（qRT-PCR）验证了观察到的差异基因表达模式的可靠性。此外，在接种菌株 MYSP113 后，植物根中的过氧化物酶和超氧化物歧化酶等植物酶活性显著增加。研究结果有助于理解植物促生根际细菌与植物的相互作用。
