Gene Expression
Nebulas
Gene Expression Nebulas概要: We report about the effects of temperature increase on rice response to Xanthomonas oryzae pv. oryzae using high throughput sequencing (RNA-Seq). The time course transcriptomic analysis revealed that temperature enhanced IRBB67 resistance to combined heat and Xoo. Our findings highlight altered cellular compartment by Xoo and heat stress in both susceptible (IR24) and the resistant (IRBB67). Interestingly, up-regulation of trehalose-6-phosphatase gene and low affinity cation transporter in IRBB67 suggest that IRBB67 maintained a certain homeostasis under high temperature to have its resistance enhanced. The interplay of both heat stress and Xoo responses as determined by up-regulated and down-regulated genes demonstrates how resistant plant cope with combined biotic and abiotic stresses. This study provides an understanding of how IRBB67 mediated resistance to Xoo under temperature get insight to cross talk in abiotic and biotic stress regulatory pathway.
项目整体设计: Leaf mRNA profile of 21 days old plants of IR24 (susceptible) and IRBB67 (resistant) inoculated with Xanthomonas oryzae pv. oryzae strain PXO145 under two temperature regimes. Samples were collected at three time points (3hours post inoculation, hpi; 72 hpi and 120 hpi).
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| 生长方案: | Rice genotypes IR24 (susceptible), and IRBB67 (Xa4+Xa7) seeds were pre-germinated for 4 days at 37°C and transferred in pot for further growth under greenhouse conditions (12h light and 12h dark). Two weeks old healthy plants were then transferred into indoor growth chambers under two temperature regimes (29/21 °C and 35/31 °C; day/night temperatures) and 70% of relative humidity and inoculated at 21 days old. Philippines Xoo race 7, strain PXO145 (avrXa4+avrXa7) inoculums was prepared from 3 days old culture. Seedling of IR24 and IRBB67 at 21 days old were syringe needless inoculated with PXO145 and sterilized demineralized water (Mock) for RNA-Seq gene expression analysis. Leaf at the second position of the main tiller was inoculated and leaves were sampled at 3, 72 and 120 hours post inoculation (hpi). A pulled leaves from 5 plants for each rice genotype treatment at each time point and immediately frozen in liquid nitrogen, and stored at -80°C until total RNA extraction. |
| 处理方案: | Twenty-one day-old seedlings of IR24, IRBB4, IRBB7 and IRBB67 were inoculated by the leaf clipping method78 while IR24 and IRBB67 plants were inoculated at 3 points of infiltration using syringe needless with PXO145 and with sterilized demineralized water (mock). |
| 提取方案: | Total RNA was extracted from syringe needless inoculated leaves using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer protocol. Total RNA was then treated with DNase (Promega) and quantified using NanoDrop. RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). For each time point and condition, two biological replicates and cleaned total RNA. |
| 建库方案: | Libraries were prepared according to Illumina's instructions. Briefly, Single-end fragment library of 100bp length was generated from cleaned total RNA following the TruSeq RNA Sample Preparation kit. Cluster generation of the produced libraries was performed using Illumina_ TruSeq SR Cluster Kit v3 - cBot - HS, and sequenced on a HiSeq 2000 platform (Illumina) with single-end 100-bp reads. |
| 分子类型: | poly(A)+ RNA |
| 库的片段类型: | SINGLE |
| 库的链类型: | - |
| 测序平台: | ILLUMINA |
| 测序仪型号: | Illumina HiSeq 2000 |
| 链特异性: | Unspecific |
| 数据来源 | GEN样本编号 | GEN数据集编号 | 系列编号 | 项目编号 | 样本编号 | 样本名称 | 生物样本编号 | 样本访问号 | 实验访问号 | 释放时间 | 提交时间 | 最后更新时间 | 物种 | 种族 | 族裔 | 年龄 | 年龄单位 | 性别 | 来源名称 | 组织 | 细胞类型 | 细胞亚型 | 细胞系 | 疾病 | 疾病状态 | 发育阶段 | 突变/变异 | 表型 | Condition Detail | 生长方案 | 处理方案 | 提取方案 | 建库方案 | 分子类型 | 库的片段类型 | 链特异性 | 库的链类型 | 加标（Spike-In） | 测序方法 | 测序平台 | 测序仪型号 | 细胞数 | 测序片段数 | 碱基数 | 平均测序片段长度_1 | 平均测序片段长度_2 | 唯一比对率 | 多重比对率 | 覆盖度 |
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