Differentially expressed proteins during an incompatible interaction between common bean and the fungus Pseudocercospora griseola

The common bean (Phaseolus vulgaris L.) is the main source of protein and an important source of minerals in several countries around the world. Angular leaf spot, caused by the fungus Pseudocercospora griseola, is one of the major diseases of the common bean. In this work, we used two-dimensional gel electrophoresis and mass spectrometry to analyze alterations in the proteome of common bean leaves challenged with an incompatible race of P. griseola. Twenty-three differentially expressed proteins were detected in leaves of cultivar AND 277 collected at 12, 24 and 48 h after inoculation. The proteins were digested with trypsin and submitted to MALDI-TOF/TOF and MicrOTOF-Q electrospray mass spectrometry. Nineteen of them were identified upon MS/MS fragmentation. Most of these proteins are involved with amino acid metabolism, terpenoid metabolism, phenylpropanoid biosynthesis, antioxidant systems, vitamin and cofactor metabolism, plant–pathogen interaction, carbohydrate metabolism, photosynthesis, or genetic information processing, showing that the interaction in this pathosystem affects different genes from various metabolic pathways and processes.     

Genome-wide transcriptional changes of ramie (Boehmeria nivea L. Gaud) in response to root-lesion nematode infection

Ramie fiber extracted from stem bark is one of the most important natural fibers. The root-lesion nematode (RLN) Pratylenchus coffeae is a major ramie pest and causes large fiber yield losses in China annually. The response mechanism of ramie to RLN infection is poorly understood. In this study, we identified genes that are potentially involved in the RLN-resistance in ramie using Illumina pair-end sequencing in two RLN-infected plants (Inf1 and Inf2) and two control plants (CO1 and CO2). Approximately 56.3, 51.7, 43.4, and 45.0 million sequencing reads were generated from the libraries of CO1, CO2, Inf1, and Inf2, respectively. De novo assembly for these 196 million reads yielded 50,486 unigenes with an average length of 853.3 bp. A total of 24,820 (49.2%) genes were annotated for their function. Comparison of gene expression levels between CO and Inf ramie revealed 777 differentially expressed genes (DEGs). The expression levels of 12 DEGs were further confirmed by real-time quantitative PCR (qRT-PCR). Pathway enrichment analysis showed that three pathways (phenylalanine metabolism, carotenoid biosynthesis, and phenylpropanoid biosynthesis) were strongly influenced by RLN infection. A series of candidate genes and pathways that may contribute to the defense response against RLN in ramie will be helpful for further improving resistance to RLN infection.     

Comparative analysis reveals changes in transcriptomes of sugarcane upon infection by Leifsoniaxyli subsp. xyli

Ratoon stunting disease (RSD) caused by bacterium Leifsoniaxyli subsp. xyli (Lxx) is a devastating disease of sugarcane over a large part of the world. Genetic improvement for RSD‐resistant varieties is considered the most effective method to control the disease. However, genetic improvement of sugarcane is hindered by the limited information about the molecular mechanisms underlying Lxx pathogenicity and defence responses in sugarcane. In this study, genome‐wide gene expression profiling was used to compare RSD‐resistant (CP72‐2086) and RSD‐susceptible (GT11) genotypes at different infection time points in order to identify the candidate regulators for RSD resistance. A total of 14,494 differentially expressed genes (DEGs) were identified, indicating that dramatic changes had occurred in gene expression upon Lxx infection, especially in the susceptible genotype. Enrichment analysis showed that a large number of genes related to plant hormone signal transduction, phenylalanine metabolism, phenylpropanoid biosynthesis and starch and sucrose metabolism was responsible for sugarcane response to Lxx infection. Plant hormone signalling pathway genes were significantly differentially expressed at the early infection stage between the two genotypes. The resistant genotype chose the jasmonic acid‐ and ethylene‐dependent host‐defence pathways to resist Lxx infection, whereas the susceptible genotype preferred the salicylic acid‐dependent host‐defence pathways. These findings help unravel the molecular mechanisms of sugarcane plant–Lxx interactions and may pave the way for sugarcane breeding for disease resistance.     

Transcriptome analysis provides insights into lignin synthesis and MAPK signaling pathway that strengthen the resistance of bitter gourd (Momordica charantia) to Fusarium wilt

Fusarium wilt is a typical soil-borne disease caused by Fusarium oxysporum f. sp. momordicae (FOM) in bitter gourd. In this study, by comparing sequencing data at multiple time points and considering the difference between resistant (R) and susceptible (S) varieties, differentially expressed genes were screened out. Short time-series expression miner analysis revealed the upregulated expression trend of genes, which were enriched in phenylpropanoid biosynthesis, plant–pathogen interaction, and mitogen-activated protein kinase signaling pathway. Further, observation of the microstructure revealed that the R variety may form tyloses earlier than the S variety to prevent mycelium diffusion from the xylem vessel. After Fusarium wilt infection, the enzymatic activities of superoxide dismutase, peroxidase, phenylalanine ammonia lyase, and catalaseas well as levels of superoxide anion and malondialdehyde were increased in the R variety higher than those in the S variety. This study provides a reference to elucidate the disease resistance mechanism of bitter gourd.     

不同抗逆性菠萝品种的差异基因和差异代谢物分析

该研究对2个不同抗逆性的菠萝品种PZ2(抗逆性较差)和PZ3(抗逆性强)进行转录组和代谢组比较分析,以探索品种间抗逆性差异的分子生理机制,为菠萝抗性育种提供理论依据。(1)转录组结果显示,以PZ2为对照,在2个品种间共筛选到1 667个差异表达基因,上调和下调的差异表达基因分别为770个和897个;其中筛选到20个与抗逆性相关的差异表达基因,包括WRKY和MYB转录因子基因以及ASR3、SOD1、POD48、HSP20、GSTF1、GSTU17等基因。(2)代谢组分析表明,以PZ2为对照,在2个品种间共筛选到208个差异代谢物,含量上调和下调的差异代谢物分别为98个和110个,其中22种差异代谢物与抗逆性相关,包括氨基酸及其衍生物、脂类、黄酮类、糖类和糖苷等。(3)qRT PCR分析验证表明,所选的8个差异表达基因在菠萝品种PZ2与PZ3中的差异表达趋势与转录组测序中差异基因表达水平变化趋势基本一致。(4)关联分析表明,差异表达基因和差异代谢物共同富集的通路有类黄酮生物合成,苯丙素生物合成,莨宕烷、哌啶和吡啶丙酸盐生物合成,半胱氨酸与蛋氨酸代谢等4条。研究发现,抗逆性强的菠萝品种的非生物逆境反应相关基因、抗氧化酶基因、逆境响应结构基因和调控基因的表达水平高于抗逆性较差的品种,且黄酮类、氨基酸衍生物类及木脂素、脂质等代谢物的含量也高于抗逆性较差的品种。     

Global gene expression responses to waterlogging in roots of sesame (Sesamum indicum L.)

Waterlogging stress lowers yields in sesame (Sesamum indicum L.). A major component of waterlogging stress is the lack of oxygen available to submerged tissues. Although the morphology and physiology of plants grown under anaerobic conditions have been studied in detail, limited work has been done to elucidate adaptations at the molecular level. To gain comprehensive insight into how sesame responds to hypoxia at the genome level, we performed gene expression profiling at two time points during a 36-h period following hypoxic treatment using a whole-genome RNA-Seq analysis. We identified sets of significantly positively and negatively expressed genes (induced and repressed, respectively) in response to hypoxia with distinct temporal profiles. The genes that were affected were associated with glycolysis, nitrogen metabolism, starch and sucrose metabolism and plant hormone signal transduction and indicated the upregulation of particular pathways (glycolysis/glycogenesis) in the Kyoto Encyclopedia of Genes and Genomes. Moreover, significant changes in the expression of genes were found for pathways, including flavone and flavonol biosynthesis, steroid biosynthesis, photosynthesis, cysteine and methionine metabolism, glutathione metabolism, as well as phenylpropanoid biosynthesis, spliceosome, circadian rhythm. This study helps in elucidating the molecular mechanisms of waterlogging tolerance and provides a basis for the genetic engineering of sesame.     

拟南芥不定芽发生早期的数字基因表达谱分析

目前,有关不定芽发生的研究主要集中在单基因的调控方面,缺乏转录组方面的系统研究.利用RNA-seq高通量测序技术在全基因组范围内检测了不定芽发生早期的基因表达谱,共检测到2457个差异表达基因.这些基因参与了激素代谢和信号转导、愈伤组织和侧根的形成、茎顶端分生组织的发育和光合作用等过程.进一步的途径富集分析表明,不定芽发生早期苯丙氨酸代谢和苯丙胺素合成等途径相关的基因显著富集.并且苯丙氨酸可以显著抑制不定芽的发生,暗示了苯丙氨酸代谢和苯丙胺素的合成可能在不定芽发生过程起着重要的作用.