Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran.
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia.
PLoS One. 2018 Apr 10;13(4):e0194592. doi: 10.1371/journal.pone.0194592. eCollection 2018.
Maize Iranian mosaic virus (MIMV, genus Nucleorhabdovirus, family Rhabdoviridae) causes an economically important disease in maize and other gramineous crops in Iran. MIMV negative-sense RNA genome sequence of 12,426 nucleotides has recently been completed. Maize Genetics and Genomics database shows that 39,498 coding genes and 4,976 non-coding genes of maize have been determined, but still some transcripts could not be annotated. The molecular host cell responses of maize to MIMV infection including differential gene expression have so far not been elucidated.
METHODOLOGY/PRINCIPAL FINDINGS: Complementary DNA libraries were prepared from total RNA of MIMV-infected and mock-inoculated maize leaves and sequenced using Illumina HiSeq 2500. Cleaned raw transcript reads from MIMV-infected maize were mapped to reads from uninfected maize and to a maize reference genome. Differentially expressed transcripts were characterized by gene ontology and biochemical pathway analyses. Transcriptome data for selected genes were validated by real-time quantitative PCR.
CONCLUSION/SIGNIFICANCE: Approximately 42 million clean reads for each treatment were obtained. In MIMV-infected maize compared to uninfected plants, 1689 transcripts were up-regulated and 213 transcripts were down-regulated. In response to MIMV infection, several pathways were activated in maize including immune receptor signaling, metabolic pathways, RNA silencing, hormone-mediated pathways, protein degradation, protein kinase and ATP binding activity, and fatty acid metabolism. Also, several transcripts including those encoding hydrophobic protein RCI2B, adenosylmethionine decarboxylase NAC transcription factor and nucleic acid binding, leucine-rich repeat, heat shock protein, 26S proteasome, oxidoreductases and endonuclease activity protein were up-regulated. These data will contribute to the identification of genes and pathways involved in plant-virus interactions that may serve as future targets for improved disease control.
玉米伊朗 mosaic 病毒（MIMV，属核型多角体病毒，杆状病毒科）导致伊朗玉米和其他禾本科作物的一种重要经济疾病。MIMV 负义 RNA 基因组序列最近已完成，长度为 12426 个核苷酸。玉米遗传学和基因组数据库显示，玉米已确定了 39498 个编码基因和 4976 个非编码基因，但仍有一些转录本无法注释。迄今为止，尚未阐明玉米对 MIMV 感染的分子宿主细胞反应，包括差异基因表达。
方法/主要发现：从 MIMV 感染和模拟接种的玉米叶片总 RNA 制备 cDNA 文库，并使用 Illumina HiSeq 2500 进行测序。从感染 MIMV 的玉米中清洗的原始转录物读数与未感染的玉米读数以及玉米参考基因组进行了比对。通过基因本体和生化途径分析来描述差异表达的转录本。通过实时定量 PCR 验证了选定基因的转录组数据。
结论/意义：每种处理分别获得约 4200 万个清洁读数。与未感染植物相比，在感染 MIMV 的玉米中，有 1689 个转录物上调，213 个转录物下调。在对 MIMV 感染的反应中，玉米中激活了几条途径，包括免疫受体信号、代谢途径、RNA 沉默、激素介导途径、蛋白质降解、蛋白激酶和 ATP 结合活性以及脂肪酸代谢。此外，一些转录物，包括编码疏水性蛋白 RCI2B、腺苷甲硫氨酸脱羧酶 NAC 转录因子和核酸结合、亮氨酸丰富重复、热休克蛋白、26S 蛋白酶体、氧化还原酶和内切核酸酶活性蛋白的转录物上调。这些数据将有助于鉴定参与植物-病毒相互作用的基因和途径，这些基因和途径可能成为未来改善疾病控制的目标。
