Comparative transcriptome analysis between thrips-resistant and thrips-susceptible alfalfa (Medicago sativa L.)

2020 ◽  
Author(s):  
Zhiqiang Zhang ◽  
Buhe Temuer ◽  
Xiaoyu Wang ◽  
Sarula Bao ◽  
Jinyan Liu ◽  
...  
Keyword(s):  
Plant Pathogen ◽  
Molecular Mechanisms ◽  
Recurrent Selection ◽  
Acid Metabolism ◽  
Insect Pests ◽  
Plant Protection ◽  
Primary Metabolism ◽  
Significant Finding ◽  
Plant Pathogen Interaction ◽  
Upregulated Genes

Abstract Background: Thrips (Thysanoptera: Thripidae) are major insect pests on alfalfa and result in decreased plant nutrients and growth, low yields and even plant death. In our previous studies, an alfalfa variety (Caoyuan No.4) with high thrips resistance was bred through consecutive field recurrent selection. In order to better understand the genetic and molecular mechanisms of thrips resistance in Caoyuan No.4, RNA-Sequencing was employed using the thrips-resistant alfalfa accession (Caoyuan No.4) and a thrips-susceptible alfalfa accession (Caoyuan No.2), each with and without thrips infestation.Results: There were 851 genes constitutively upregulated and 434 genes downregulated in Caoyuan No.4 compared to Caoyuan No.2 without thrips infestation. The upregulated genes were mainly involved in primary metabolism such as energy metabolism and carbohydrate metabolism, lipid metabolism and certain secondary metabolites, while the downregulated genes were mainly related to plant-pathogen interaction. In addition, very few DEGs (only 13) were detected in Caoyuan No.4 after thrips stress, but a total of 3326 contigs DEGs were detected in Caoyuan No.2 after thrips stress. The upregulated genes in Caoyuan No.2 after stress were mainly involved in isoflavonoid biosynthesis, proteasome, amino sugar and nucleotide sugar metabolism, flavonoid biosynthesis as well as plant-pathogen interaction. Moreover, 117 genes that were shared in both the S_CK vs S_T group and S_CK vs R_CK group were divided into 6 clusters, which are mainly involved in secondary metabolism, fatty acid metabolism, amino acid metabolism, rust resistance kinase, WRKY transcription factor and nodule lectin.Conclusion: Both constitutive defensive genes and potential induced defensive genes were detected in the defense of Caoyuan No.4. That two distinct kinds of defensive genes — constitutive defensive genes and induced defensive genes — can be simultaneously activated and thus potentially enhance plant protection against insects attacks is a significant finding for plant resistance breeders.

scholarly journals Transcriptome analysis reveals the molecular mechanisms of response to an emergent yellow-flower disease in green Chinese prickly ash (Zanthoxylum schinifolium)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Fan Xu ◽  
Qian Meng ◽  
Xiaodong Suo ◽  
Yonghong Xie ◽  
Yueqing Cheng ◽  
...  
Keyword(s):  
Plant Pathogen ◽  
Molecular Mechanisms ◽  
Economic Losses ◽  
Molecular Response ◽  
Yellow Flower ◽  
Chongqing Municipality ◽  
Plant Pathogen Interaction ◽  
Chinese Prickly Ash ◽  
Flower Disease ◽  
Zanthoxylum Schinifolium

AbstractChinese prickly ash (Zanthoxylum) is extensively used as spice and traditional medicine in eastern Asian countries. Recently, an emergent yellow-flower disease (YFD) break out in green Chinese prickly ash (Zanthoxylum schinifolium, Qinghuajiao in Chinese) at Chongqing municipality, and then leads to a sharp reduction in the yield of Qinghuajiao, and thus results in great economic losses for farmers. To address the molecular response for the emergent YFD of Qinghuajiao, we analyzed the transcriptome of 12 samples including the leaves and inflorescences of asymptomatic and symptomatic plants from three different towns at Chongqing by high-throughput RNA-Seq technique. A total of 126,550 genes and 229,643 transcripts were obtained, and 21,054 unigenes were expressed in all 12 samples. There were 56 and 164 different expressed genes (DEGs) for the AL_vs_SL (asymptomatic leaf vs symptomatic leaf) and AF_vs_SF (asymptomatic flower vs symptomatic flower) groups, respectively. The results of KEGG analysis showed that the “phenylpropanoid biosynthesis” pathway that related to plant–pathogen interaction were found in AL_vs_SL and AF_vs_SF groups, and the “Plant–pathogen interaction” found in AF_vs_SF group, implying that this Qinghuajiao YFD might cause by plant pathogen. Interestingly, we detected 33 common unigenes for the 2 groups, and almost these unigenes were up-regulated in the symptomatic plants. Moreover, most of which were homologs to virus RNA, the components of viruses, implying that this YFD was related to virus. Our results provided a primary molecular basis for the prevention and treatment of YFD of Qinghuajiao trees.

scholarly journals Metabolome and Transcriptome Analysis of the Response Mechanisms of Ginseng to Rust Root Symptoms

2021 ◽  
Author(s):  
Xingbo Bian ◽  
Yan Zhao ◽  
Shengyuan Xiao ◽  
He Yang ◽  
Yongzhong Han ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcriptome Analysis ◽  
Plant Pathogen ◽  
Molecular Mechanisms ◽  
Plant Hormone ◽  
Vital Role ◽  
Mechanism Model ◽  
Phenylpropanoid Biosynthesis ◽  
Plant Pathogen Interaction

Abstract Background: Ginseng rusty root symptoms (GRS) is one of the primary diseases of ginseng. It leads to a severe decline in the quality of ginseng. Results: Compared with Healthy ginseng (HG), 949 metabolites and 9451 genes in diseased tissues were significantly changed at the metabolic and transcription levels. The metabolic patterns of the diseased tissues changed significantly, and organic acids, alkaloids, alcohols, and phenols may play a vital role in the response of ginseng to this disease. There were significant differences in the expression of plant hormone signal transduction, phenylpropanoid biosynthesis, peroxidase pathway, and multiple genes in the plant-pathogen interaction pathway.Conclusion: The current study performed a comparative metabolome and transcriptome analysis of GRS and HG. Based on the findings at the transcriptional and metabolic levels, the mechanism model of ginseng response to rusty root symptoms was established. Our results provide new insights into ginseng's response to rusty root symptoms, which will help reveal the potential molecular mechanisms of this disease in ginseng.

scholarly journals Understanding Plant Social Networking System: Avoiding Deleterious Microbiota but Calling Beneficials

2021 ◽  
Vol 22 (7) ◽  
pp. 3319
Author(s):  
Yong-Soon Park ◽  
Choong-Min Ryu
Keyword(s):  
Social Networking ◽  
Molecular Mechanisms ◽  
Insect Pests ◽  
Plant Protection ◽  
Plant Immunity ◽  
Microbial Pathogens ◽  
Beneficial Microbes ◽  
Microbial Association ◽  
Active Involvement ◽  
Survival Potential

Plant association with microorganisms elicits dramatic effects on the local phytobiome and often causes systemic and transgenerational modulation on plant immunity against insect pests and microbial pathogens. Previously, we introduced the concept of the plant social networking system (pSNS) to highlight the active involvement of plants in the recruitment of potentially beneficial microbiota upon exposure to insects and pathogens. Microbial association stimulates the physiological responses of plants and induces the development of their immune mechanisms while interacting with multiple enemies. Thus, beneficial microbes serve as important mediators of interactions among multiple members of the multitrophic, microscopic and macroscopic communities. In this review, we classify the steps of pSNS such as elicitation, signaling, secreting root exudates, and plant protection; summarize, with evidence, how plants and beneficial microbes communicate with each other; and also discuss how the molecular mechanisms underlying this communication are induced in plants exposed to natural enemies. Collectively, the pSNS modulates robustness of plant physiology and immunity and promotes survival potential by helping plants to overcome the environmental and biological challenges.

scholarly journals Plant SWEETs: from sugar transport to plant–pathogen interaction and more unexpected physiological roles

2021 ◽  
Author(s):  
Richard Breia ◽  
Artur Conde ◽  
Hélder Badim ◽  
Ana Margarida Fortes ◽  
Hernâni Gerós ◽  
...  
Keyword(s):  
Plant Pathogen ◽  
Sugar Transport ◽  
High Capacity ◽  
Phloem Loading ◽  
Transcription Activator ◽  
Pythium Irregulare ◽  
Clear Cut ◽  
Opposite Behavior ◽  
Plant Pathogen Interaction ◽  
Plant Pathogen Interactions

Abstract Sugars Will Eventually be Exported Transporters (SWEETs) have important roles in numerous physiological mechanisms where sugar efflux is critical, including phloem loading, nectar secretion, seed nutrient filling, among other less expected functions. They mediate low affinity and high capacity transport, and in angiosperms this family is composed by 20 paralogs on average. As SWEETs facilitate the efflux of sugars, they are highly susceptible to hijacking by pathogens, making them central players in plant–pathogen interaction. For instance, several species from the Xanthomonas genus are able to upregulate the transcription of SWEET transporters in rice (Oryza sativa), upon the secretion of transcription-activator-like effectors. Other pathogens, such as Botrytis cinerea or Erysiphe necator, are also capable of increasing SWEET expression. However, the opposite behavior has been observed in some cases, as overexpression of the tonoplast AtSWEET2 during Pythium irregulare infection restricted sugar availability to the pathogen, rendering plants more resistant. Therefore, a clear-cut role for SWEET transporters during plant–pathogen interactions has so far been difficult to define, as the metabolic signatures and their regulatory nodes, which decide the susceptibility or resistance responses, remain poorly understood. This fuels the still ongoing scientific question: what roles can SWEETs play during plant–pathogen interaction? Likewise, the roles of SWEET transporters in response to abiotic stresses are little understood. Here, in addition to their relevance in biotic stress, we also provide a small glimpse of SWEETs importance during plant abiotic stress, and briefly debate their importance in the particular case of grapevine (Vitis vinifera) due to its socioeconomic impact.

scholarly journals Transcriptome Reveals Roles of Lignin-Modifying Enzymes and Abscisic Acid in the Symbiosis of Mycena and Gastrodia elata

2021 ◽  
Vol 22 (12) ◽  
pp. 6557
Author(s):  
Li-Ying Ren ◽  
Heng Zhao ◽  
Xiao-Ling Liu ◽  
Tong-Kai Zong ◽  
Min Qiao ◽  
...  
Keyword(s):  
Biological Activity ◽  
Abscisic Acid ◽  
Lignin Degradation ◽  
Molecular Mechanisms ◽  
Receptor Protein ◽  
Gastrodia Elata ◽  
Upregulated Genes ◽  
Aba Biosynthesis ◽  
Seed Coats

Gastrodia elata is a well-known medicinal and heterotrophic orchid. Its germination, limited by the impermeability of seed coat lignin and inhibition by abscisic acid (ABA), is triggered by symbiosis with fungi such as Mycena spp. However, the molecular mechanisms of lignin degradation by Mycena and ABA biosynthesis and signaling in G. elata remain unclear. In order to gain insights into these two processes, this study analyzed the transcriptomes of these organisms during their dynamic symbiosis. Among the 25 lignin-modifying enzyme genes in Mycena, two ligninolytic class II peroxidases and two laccases were significantly upregulated, most likely enabling Mycena hyphae to break through the lignin seed coats of G. elata. Genes related to reduced virulence and loss of pathogenicity in Mycena accounted for more than half of annotated genes, presumably contributing to symbiosis. After coculture, upregulated genes outnumbered downregulated genes in G. elata seeds, suggesting slightly increased biological activity, while Mycena hyphae had fewer upregulated than downregulated genes, indicating decreased biological activity. ABA biosynthesis in G. elata was reduced by the downregulated expression of 9-cis-epoxycarotenoid dioxygenase (NCED-2), and ABA signaling was blocked by the downregulated expression of a receptor protein (PYL12-like). This is the first report to describe the role of NCED-2 and PYL12-like in breaking G. elata seed dormancy by reducing the synthesis and blocking the signaling of the germination inhibitor ABA. This study provides a theoretical basis for screening germination fungi to identify effective symbionts and for reducing ABA inhibition of G. elata seed germination.

scholarly journals Genome-Wide Mapping of Histone H3 Lysine 4 Trimethylation (H3K4me3) and Its Involvement in Fatty Acid Biosynthesis in Sunflower Developing Seeds

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 706
Author(s):  
Antonio J. Moreno-Pérez ◽  
Raquel Martins-Noguerol ◽  
Cristina DeAndrés-Gil ◽  
Mónica Venegas-Calerón ◽  
Rosario Sánchez ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Chromatin Remodeling ◽  
Molecular Mechanisms ◽  
Acid Metabolism ◽  
Fatty Acid Biosynthesis ◽  
Acid Synthesis ◽  
Sunflower Seeds ◽  
Acid Biosynthesis ◽  
Functional Regions ◽  
Genome Wide

Histone modifications are of paramount importance during plant development. Investigating chromatin remodeling in developing oilseeds sheds light on the molecular mechanisms controlling fatty acid metabolism and facilitates the identification of new functional regions in oil crop genomes. The present study characterizes the epigenetic modifications H3K4me3 in relationship with the expression of fatty acid-related genes and transcription factors in developing sunflower seeds. Two master transcriptional regulators identified in this analysis, VIV1 (homologous to Arabidopsis ABI3) and FUS3, cooperate in the regulation of WRINKLED 1, a transcriptional factor regulating glycolysis, and fatty acid synthesis in developing oilseeds.

scholarly journals 3D-surface MALDI mass spectrometry imaging for visualising plant defensive cardiac glycosides in Asclepias curassavica

2021 ◽  
Vol 413 (8) ◽  
pp. 2125-2134
Author(s):  
Domenic Dreisbach ◽  
Georg Petschenka ◽  
Bernhard Spengler ◽  
Dhaka R. Bhandari
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Imaging ◽  
Cardiac Glycosides ◽  
Molecular Mechanisms ◽  
Plant Science ◽  
Primary Metabolism ◽  
Native Plant ◽  
Asclepias Curassavica ◽  
3D Surface ◽  
3D Surfaces

AbstractMass spectrometry–based imaging (MSI) has emerged as a promising method for spatial metabolomics in plant science. Several ionisation techniques have shown great potential for the spatially resolved analysis of metabolites in plant tissue. However, limitations in technology and methodology limited the molecular information for irregular 3D surfaces with resolutions on the micrometre scale. Here, we used atmospheric-pressure 3D-surface matrix-assisted laser desorption/ionisation mass spectrometry imaging (3D-surface MALDI MSI) to investigate plant chemical defence at the topographic molecular level for the model system Asclepias curassavica. Upon mechanical damage (simulating herbivore attacks) of native A. curassavica leaves, the surface of the leaves varies up to 700 μm, and cardiac glycosides (cardenolides) and other defence metabolites were exclusively detected in damaged leaf tissue but not in different regions of the same leaf. Our results indicated an increased latex flow rate towards the point of damage leading to an accumulation of defence substances in the affected area. While the concentration of cardiac glycosides showed no differences between 10 and 300 min after wounding, cardiac glycosides decreased after 24 h. The employed autofocusing AP-SMALDI MSI system provides a significant technological advancement for the visualisation of individual molecule species on irregular 3D surfaces such as native plant leaves. Our study demonstrates the enormous potential of this method in the field of plant science including primary metabolism and molecular mechanisms of plant responses to abiotic and biotic stress and symbiotic relationships. Graphical abstract

scholarly journals Insights into how environment shapes post-mortem RNA transcription in mouse brain

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Raphael Severino Bonadio ◽  
Larissa Barbosa Nunes ◽  
Patricia Natália S. Moretti ◽  
Juliana Forte Mazzeu ◽  
Stefano Cagnin ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Mouse Brain ◽  
Molecular Mechanisms ◽  
Cell Communication ◽  
Rna Degradation ◽  
The Body ◽  
Biological Processes ◽  
Post Mortem ◽  
Gene Expression Alterations ◽  
Upregulated Genes

AbstractMost biological features that occur on the body after death were already deciphered by traditional medicine. However, the molecular mechanisms triggered in the cellular microenvironment are not fully comprehended yet. Previous studies reported gene expression alterations in the post-mortem condition, but little is known about how the environment could influence RNA degradation and transcriptional regulation. In this work, we analysed the transcriptome of mouse brain after death under three concealment simulations (air exposed, buried, and submerged). Our analyses identified 2,103 genes differentially expressed in all tested groups 48 h after death. Moreover, we identified 111 commonly upregulated and 497 commonly downregulated genes in mice from the concealment simulations. The gene functions shared by the individuals from the tested environments were associated with RNA homeostasis, inflammation, developmental processes, cell communication, cell proliferation, and lipid metabolism. Regarding the altered biological processes, we identified that the macroautophagy process was enriched in the upregulated genes and lipid metabolism was enriched in the downregulated genes. On the other hand, we also described a list of biomarkers associated with the submerged and buried groups, indicating that these environments can influence the post-mortem RNA abundance in its particular way.

scholarly journals Integrative iTRAQ-based proteomic and transcriptomic analysis reveals the accumulation patterns of key metabolites associated with oil quality during seed ripening of Camellia oleifera

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Zhouchen Ye ◽  
Jing Yu ◽  
Wuping Yan ◽  
Junfeng Zhang ◽  
Dongmei Yang ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Molecular Mechanisms ◽  
Acid Metabolism ◽  
Oil Quality ◽  
Gas Chromatography Mass Spectrometry ◽  
Glutathione Metabolism ◽  
Poor Correlation ◽  
Camellia Oleifera ◽  
Specific Expression

AbstractCamellia oleifera (C. oleifera) is one of the four major woody oil-bearing crops in the world and has relatively high ecological, economic, and medicinal value. Its seeds undergo a series of complex physiological and biochemical changes during ripening, which is mainly manifested as the accumulation and transformation of certain metabolites closely related to oil quality, especially flavonoids and fatty acids. To obtain new insights into the underlying molecular mechanisms, a parallel analysis of the transcriptome and proteome profiles of C. oleifera seeds at different maturity levels was conducted using RNA sequencing (RNA-seq) and isobaric tags for relative and absolute quantification (iTRAQ) complemented with gas chromatography-mass spectrometry (GC-MS) data. A total of 16,530 transcripts and 1228 proteins were recognized with significant differential abundances in pairwise comparisons of samples at various developmental stages. Among these, 317 were coexpressed with a poor correlation, and most were involved in metabolic processes, including fatty acid metabolism, α-linolenic acid metabolism, and glutathione metabolism. In addition, the content of total flavonoids decreased gradually with seed maturity, and the levels of fatty acids generally peaked at the fat accumulation stage; these results basically agreed with the regulation patterns of genes or proteins in the corresponding pathways. The expression levels of proteins annotated as upstream candidates of phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) as well as their cognate transcripts were positively correlated with the variation in the flavonoid content, while shikimate O-hydroxycinnamoyltransferase (HCT)-encoding genes had the opposite pattern. The increase in the abundance of proteins and mRNAs corresponding to alcohol dehydrogenase (ADH) was associated with a reduction in linoleic acid synthesis. Using weighted gene coexpression network analysis (WGCNA), we further identified six unique modules related to flavonoid, oil, and fatty acid anabolism that contained hub genes or proteins similar to transcription factors (TFs), such as MADS intervening keratin-like and C-terminal (MIKC_MADS), type-B authentic response regulator (ARR-B), and basic helix-loop-helix (bHLH). Finally, based on the known metabolic pathways and WGCNA combined with the correlation analysis, five coexpressed transcripts and proteins composed of cinnamyl-alcohol dehydrogenases (CADs), caffeic acid 3-O-methyltransferase (COMT), flavonol synthase (FLS), and 4-coumarate: CoA ligase (4CL) were screened out. With this exploratory multiomics dataset, our results presented a dynamic picture regarding the maturation process of C. oleifera seeds on Hainan Island, not only revealing the temporal specific expression of key candidate genes and proteins but also providing a scientific basis for the genetic improvement of this tree species.

Sign in / Sign up

Export Citation Format

Share Document