scholarly journals Phytophthora infestans RXLR effector Pi04089 perturbs diverse defense-related genes to suppress host immunity

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ming Luo ◽  
Xinyuan Sun ◽  
Yetong Qi ◽  
Jing Zhou ◽  
Xintong Wu ◽  
...  
Keyword(s):  
Phytophthora Infestans ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Host Immunity ◽  
Host Cells ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
Host Immune Responses ◽  
Potato Plants ◽  
Rxlr Effector

Abstract Background The oomycete pathogen secretes many effectors into host cells to manipulate host defenses. For the majority of effectors, the mechanisms related to how they alter the expression of host genes and reprogram defenses are not well understood. In order to investigate the molecular mechanisms governing the influence that the Phytophthora infestans RXLR effector Pi04089 has on host immunity, a comparative transcriptome analysis was conducted on Pi04089 stable transgenic and wild-type potato plants. Results Potato plants stably expressing Pi04089 were more susceptible to P. infestans. RNA-seq analysis revealed that 658 upregulated genes and 722 downregulated genes were characterized in Pi04089 transgenic lines. A large number of genes involved in the biological process, including many defense-related genes and certain genes that respond to salicylic acid, were suppressed. Moreover, the comparative transcriptome analysis revealed that Pi04089 significantly inhibited the expression of many flg22 (a microbe-associated molecular pattern, PAMP)-inducible genes, including various Avr9/Cf-9 rapidly elicited (ACRE) genes. Four selected differentially expressed genes (StWAT1, StCEVI57, StKTI1, and StP450) were confirmed to be involved in host resistance against P. infestans when they were transiently expressed in Nicotiana benthamiana. Conclusion The P. infestans effector Pi04089 was shown to suppress the expression of many resistance-related genes in potato plants. Moreover, Pi04089 was found to significantly suppress flg22-triggered defense signaling in potato plants. This research provides new insights into how an oomycete effector perturbs host immune responses at the transcriptome level.

scholarly journals Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 341
Author(s):  
Lei Zhang ◽  
Haoyun Sun ◽  
Tao Xu ◽  
Tianye Shi ◽  
Zongyun Li ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Morphological Analysis ◽  
Molecular Mechanisms ◽  
Flavonoid Biosynthesis ◽  
Phenotypic Characterization ◽  
Comparative Transcriptome ◽  
Hub Genes ◽  
Breeding Programs ◽  
Comparative Transcriptome Analysis ◽  
Key Pathways

Eggplant is one of the most important vegetables worldwide. Prickles on the leaves, stems and fruit calyxes of eggplant may cause difficulties during cultivation, harvesting and transportation, and therefore is an undesirable agronomic trait. However, limited knowledge about molecular mechanisms of prickle morphogenesis has hindered the genetic improvement of eggplant. In this study, we performed the phenotypic characterization and transcriptome analysis on prickly and prickleless eggplant genotypes to understand prickle development at the morphological and molecular levels. Morphological analysis revealed that eggplant prickles were multicellular, lignified and layered organs. Comparative transcriptome analysis identified key pathways and hub genes involved in the cell cycle as well as flavonoid biosynthetic, photosynthetic, and hormone metabolic processes during prickle development. Interestingly, genes associated with flavonoid biosynthesis were up-regulated in developing prickles, and genes associated with photosynthesis were down-regulated in developing and matured prickles. It was also noteworthy that several development-related transcription factors such as bHLH, C2H2, MYB, TCP and WRKY were specifically down- or up-regulated in developing prickles. Furthermore, four genes were found to be differentially expressed within the Pl locus interval. This study provides new insights into the regulatory molecular mechanisms underlying prickle morphogenesis in eggplant, and the genes identified might be exploited in breeding programs to develop prickleless eggplant cultivars.

scholarly journals Comparative transcriptome analysis indicates that a core transcriptional network mediates isonuclear alloplasmic male sterility in wheat (Triticum aestivum L.)

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Zihan Liu ◽  
Sha Li ◽  
Wei Li ◽  
Qi Liu ◽  
Lingli Zhang ◽  
...  
Keyword(s):  
Male Sterility ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Interaction Mechanism ◽  
Outer Wall ◽  
Comparative Transcriptome ◽  
Male Sterile ◽  
Comparative Transcriptome Analysis ◽  
The Impact

Abstract Background Cytoplasmic male sterility (CMS) plays a crucial role in the utilization of heterosis and various types of CMS often have different abortion mechanisms. Therefore, it is important to understand the molecular mechanisms related to anther abortion in wheat, which remain unclear at present. Results In this study, five isonuclear alloplasmic male sterile lines (IAMSLs) and their maintainer were investigated. Cytological analysis indicated that the abortion type was identical in IAMSLs, typical and stainable abortion, and the key abortive period was in the binucleate stage. Most of the 1,281 core shared differentially expressed genes identified by transcriptome sequencing compared with the maintainer in the vital abortive stage were involved in the metabolism of sugars, oxidative phosphorylation, phenylpropane biosynthesis, and phosphatidylinositol signaling, and they were downregulated in the IAMSLs. Key candidate genes encoding chalcone--flavonone isomerase, pectinesterase, and UDP-glucose pyrophosphorylase were screened and identified. Moreover, further verification elucidated that due to the impact of downregulated genes in these pathways, the male sterile anthers were deficient in sugar and energy, with excessive accumulations of ROS, blocked sporopollenin synthesis, and abnormal tapetum degradation. Conclusions Through comparative transcriptome analysis, an intriguing core transcriptome-mediated male-sterility network was proposed and constructed for wheat and inferred that the downregulation of genes in important pathways may ultimately stunt the formation of the pollen outer wall in IAMSLs. These findings provide insights for predicting the functions of the candidate genes, and the comprehensive analysis of our results was helpful for studying the abortive interaction mechanism in CMS wheat.

scholarly journals Comparative Transcriptome Analysis Reveals Related Regulatory Mechanisms of Androgenic Gland in Eriocheir sinensis

2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Chunpeng Fu ◽  
Qifan Zeng ◽  
Fajun Li ◽  
Huicui Wang ◽  
Jian Sun ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Eriocheir Sinensis ◽  
Regulatory Mechanisms ◽  
Receptor Interaction ◽  
Regulation Mechanism ◽  
Androgenic Gland ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
Mitten Crab

Chinese mitten crab (Eriocheir sinensis) is one of the most commercially important aquaculture species in China. The androgenic gland (AG) of crustaceans plays pivotal roles in the regulation of male differentiation and in maintaining the male sexual characteristics. In order to reveal related mechanisms in AG, we compared transcriptomes of AG between proliferation and secretion phase. A total of 72,000 unigenes and 4,027 differentially expressed genes were obtained. Gene ontology enrichment analysis indicated that biological processes and metabolic pathways related to protein synthesis and secretion such as transcription, translation, and signal transduction were significantly enriched. Critical genes such as IAG, SXL, TRA-2, SRY, FTZ-F1, FOXL2, and FEM-1 were identified and potentially involved in maintaining the testis development and spermatogenesis. Ribosomes pathway revealed the cause of insulin-like androgenic gland hormone secretion increase. Three insulin-like receptors were thought to be associated with growth and spermatogenesis. In the neuroactive ligand-receptor interaction pathway, the expression of octopamine receptor, 5-HT receptor 1, and melatonin receptor was significantly changed, which revealed the key regulation mechanism of aggressive and mating behavior of males. Comparative transcriptome analysis provided new insights into the genome-wide molecular mechanisms of AG development and the regulatory mechanisms of male development.

scholarly journals Comparative Transcriptome Analysis of Genes Involved in Sesquiterpene Alkaloid Biosynthesis in Trichoderma longibrachiatum MD33 and UN32

2021 ◽  
Vol 12 ◽  
Author(s):  
Xu Qian ◽  
Hui Jin ◽  
Zhuojun Chen ◽  
Qingqing Dai ◽  
Surendra Sarsaiya ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Genetic Network ◽  
Industrial Applications ◽  
Differentially Expressed ◽  
Comparative Transcriptome ◽  
Mva Pathway ◽  
Trichoderma Longibrachiatum ◽  
Comparative Transcriptome Analysis ◽  
Nitrogen Ion

Trichoderma longibrachiatum MD33, a sesquiterpene alkaloid-producing endophyte isolated from Dendrobium nobile, shows potential medical and industrial applications. To understand the molecular mechanisms of sesquiterpene alkaloids production, a comparative transcriptome analysis was performed on strain MD33 and its positive mutant UN32, which was created using Ultraviolet (UV) mutagenesis and nitrogen ion (N+) implantation. The alkaloid production of UN32 was 2.62 times more than that of MD33. One thousand twenty-four differentially expressed genes (DEGs), including 519 up-regulated and 505 down-regulated genes, were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed 139 GO terms and 87 biosynthesis pathways. Dendrobine, arguably the main sesquiterpene alkaloid the strain MD33 produced, might start synthesis through the mevalonate (MVA) pathway. Several MVA pathway enzyme-coding genes (hydroxy-methylglutaryl-CoA synthase, mevalonate kinase, and farnesyl diphosphate synthase) were found to be differentially expressed, suggesting that physical mutagenesis can disrupt genome integrity and gene expression. Some backbone post-modification enzymes and transcript factors were either discovered, suggesting the sesquiterpene alkaloid metabolism in T. longibrachiatum is a complex genetic network. Our findings help to shed light on the underlying molecular regulatory mechanism of sesquiterpene alkaloids production in T. longibrachiatum.

scholarly journals Comparative transcriptome analysis by Tilletia horrida infection in resistant and susceptible rice (Oryza sativa L.) male sterile lines reveals candidate genes and resistant mechanisms

2019 ◽  
Author(s):  
Aijun Wang ◽  
Desuo Yin ◽  
Xinyue Shu ◽  
Linxia Wang ◽  
Ping Li ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Unsaturated Fatty Acids ◽  
Oryza Sativa L ◽  
Resistance Breeding ◽  
Glutathione Metabolism ◽  
Comparative Transcriptome ◽  
Male Sterile ◽  
Comparative Transcriptome Analysis

Abstract Background Rice kernel smut (RKS), caused by the basidiomycete fungus Tilletia horrida , is one of the most devastating diseases affecting the production of male sterile lines of rice ( Oryza sativa ) worldwide. However, molecular mechanisms of resistance to T. horrida have not yet been explored.Results In the present study, analysis of the amount of T. horrida biomass in rice kernels and RNA sequencing (RNA-Seq) analysis of rice male sterile lines resistant and susceptible to RKS (Jiangcheng 3A and 9311A, respectively) were conducted after T. horrida infection. Transcriptomic analysis showed that 9, 840 and 7, 902 differentially expressed genes (DEGs) were observed in Jiangcheng3A and 9311A, respectively, after T. horrida inoculation, compared with the control. KEGG analyses of DEGs revealed that cutin, suberine and wax biosynthesis, flavonoid biosynthesis, glutathione metabolism, tyrosine metabolism, and biosynthesis of unsaturated fatty acids were enriched by T. horrida inoculation in Jiangcheng 3A; however, not significantly enriched in 9311A. Furthermore, the DEGs related to plant-pathogen interaction, plant hormone signal transduction, and transcriptional factor genes were identified in both rice male sterile lines.Conclusions This is the first comparative transcriptome analysis of two rice genotypes with different responses to T. horrida infection, revealing DEGs with potentially important roles in defense against T. horrida infection. Ours results will serve as a strong foundation for developing effective strategies for T. horrida -resistance breeding.

scholarly journals Comparative transcriptome analysis of inbred lines and contrasting hybrids reveals overdominance mediate early biomass vigor in hybrid cotton

2020 ◽  
Author(s):  
Kashif Shahzad ◽  
Xuexian Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
Huini Tang ◽  
...  
Keyword(s):  
Circadian Rhythm ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Genetic Constitution ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
Extracellular Region

Abstract Background: Heterosis breeding is the most useful method for yield increase around the globe. Heterosis is an intriguing process to develop superior offspring to either parent in the desired character. The biomass vigor produced during seedling emergence stage has a direct influence on yield heterosis in plants. Unfortunately, the genetic basis of early biomass vigor in cotton is poorly understood. Results: Three stable performing F1 hybrids varying in yield heterosis named as high, medium and low hybrids with their inbred parents were used in this study. Phenotypically, these hybrids established noticeable biomass heterosis during the early stage of seedling growth in the field. Transcriptome analysis of root and leaf revealed that hybrids showed many differentially expressed genes (DEGs) relative to their parents, while the comparison of inbred parents showed limited number of DEGs indicating similarity in their genetic constitution. Further analysis indicated expression patterns of most DEGs were overdominant in both tissues of hybrids. According to GO results, functions of overdominance genes in leaf were enriched for chloroplast, membrane, and protein binding, whereas functions of overdominance genes in root were enriched for plasma membrane, extracellular region, and responses to stress. We found several genes of circadian rhythm pathway related to LATE ELONGATED HYPOCOTYL (LHY) showed downregulated overdominant expressions in both tissues of hybrids. In addition to circadian rhythm, several leaf genes related to Aux/IAA regulation, and many root genes involved in peroxidase activity also showed overdominant expressions in hybrids. Twelve genes involved in circadian rhythm plant were selected to perform qRT-PCR analysis to confirm the accuracy of RNA-seq results. Conclusions: Through genome-wide comparative transcriptome analysis, we strongly predict that overdominance at gene expression level plays a pivotal role in early biomass vigor of hybrids. The combinational contribution of circadian rhythm and other metabolic process may control vigorous growth in hybrids. Our result provides an important foundation for dissecting molecular mechanisms of biomass vigor in hybrid cotton.

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