Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
PLoS One. 2013 Apr 30;8(4):e62460. doi: 10.1371/journal.pone.0062460. Print 2013.
The recent development of RNA sequencing (RNA-seq) technology has enabled us to analyze the transcriptomes of plants and their pathogens simultaneously. However, RNA-seq often relies on aligning reads to a reference genome and is thus unsuitable for analyzing most plant pathogens, as their genomes have not been fully sequenced. Here, we analyzed the transcriptomes of Sorghum bicolor (L.) Moench and its pathogen Bipolaris sorghicola simultaneously by using RNA-seq in combination with de novo transcriptome assembly. We sequenced the mixed transcriptome of the disease-resistant sorghum cultivar SIL-05 and B. sorghicola in infected leaves in the early stages of infection (12 and 24 h post-inoculation) by using Illumina mRNA-Seq technology. Sorghum gene expression was quantified by aligning reads to the sorghum reference genome. For B. sorghicola, reads that could not be aligned to the sorghum reference genome were subjected to de novo transcriptome assembly. We identified genes of B. sorghicola for growth of this fungus in sorghum, as well as genes in sorghum for the defense response. The genes of B. sorghicola included those encoding Woronin body major protein, LysM domain-containing intracellular hyphae protein, transcriptional factors CpcA and HacA, and plant cell-wall degrading enzymes. The sorghum genes included those encoding two receptors of the simple eLRR domain protein family, transcription factors that are putative orthologs of OsWRKY45 and OsWRKY28 in rice, and a class III peroxidase that is a homolog involved in disease resistance in the Poaceae. These defense-related genes were particularly strongly induced among paralogs annotated in the sorghum genome. Thus, in the absence of genome sequences for the pathogen, simultaneous transcriptome analysis of plant and pathogen by using de novo assembly was useful for identifying putative key genes in the plant-pathogen interaction.
最近 RNA 测序 (RNA-seq) 技术的发展使我们能够同时分析植物及其病原体的转录组。然而，RNA-seq 通常依赖于将读取与参考基因组对齐，因此不适合分析大多数植物病原体，因为它们的基因组尚未完全测序。在这里，我们通过使用 RNA-seq 结合从头转录组组装，同时分析了高粱 (L.) Moench 和其病原体偏生镰刀菌的转录组。我们使用 Illumina mRNA-Seq 技术对感染早期（接种后 12 和 24 小时）抗病高粱品种 SIL-05 和偏生镰刀菌感染叶片的混合转录组进行测序。通过将读取与高粱参考基因组对齐来量化高粱基因的表达。对于偏生镰刀菌，无法与高粱参考基因组对齐的读取进行从头转录组组装。我们鉴定了偏生镰刀菌在高粱中生长的基因，以及高粱中防御反应的基因。偏生镰刀菌的基因包括沃罗宁体主要蛋白、含 LysM 结构域的细胞内菌丝蛋白、转录因子 CpcA 和 HacA 以及植物细胞壁降解酶的基因。高粱的基因包括两个简单 eLRR 结构域蛋白家族受体的基因、水稻中推定的 OsWRKY45 和 OsWRKY28 的同源转录因子、以及参与禾本科植物抗病的 III 类过氧化物酶的基因。这些与防御相关的基因在高粱基因组注释的同源物中被强烈诱导。因此，在缺乏病原体基因组序列的情况下，使用从头组装同时对植物和病原体的转录组进行分析，有助于鉴定植物-病原体互作中的假定关键基因。
