Molecular mechanisms of growth and disease resistance in hybrid mandarin ( Siniperca chuatsi ♀ ×  Siniperca scherzeri ♂) revealed by combined miRNA‐mRNA transcriptome analysis

2022 ◽  
Author(s):  
Shuyan Ding ◽  
Yangbai Shi ◽  
Chen Hao ◽  
Guoxing Liu ◽  
Muzi Zhao ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Siniperca Chuatsi ◽  
Siniperca Scherzeri ◽  
Mrna Transcriptome

scholarly journals Insights into food preference in hybrid F1 of Siniperca chuatsi (♀) × Siniperca scherzeri (♂) mandarin fish through transcriptome analysis

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 601 ◽  
Author(s):  
Shan He ◽  
Xu-Fang Liang ◽  
Jian Sun ◽  
Ling Li ◽  
Ying Yu ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Food Preference ◽  
Mandarin Fish ◽  
Siniperca Chuatsi ◽  
Siniperca Scherzeri

Antennal transcriptome analysis and candidate olfactory genes in Crematogaster rogenhoferi

2021 ◽  
pp. 1-12
Author(s):  
Xiang Zhou ◽  
Jixing Guo ◽  
Mingxia Zhang ◽  
Chunxiu Bai ◽  
Zheng Wang ◽  
...  
Keyword(s):  
Biological Control ◽  
Transcriptome Analysis ◽  
Molecular Basis ◽  
Molecular Mechanisms ◽  
Biological Control Agent ◽  
Control Agent ◽  
Vital Role ◽  
Neuron Membrane ◽  
Ionotropic Receptors ◽  
Soft Scale

Abstract Crematogaster rogenhoferi (Hymenoptera: Formicidae), an omnivorous ant, is one of the dominant predatory natural enemies of a soft scale pest, Parasaissetia nigra Nietner (Homoptera: Coccidae), and can effectively control P. nigra populations in rubber forests. Olfaction plays a vital role in the process of predation. However, the information about the molecular mechanism of olfaction-evoked behaviour in C. rogenhoferi is limited. In this study, we conducted antennal transcriptome analysis to identify candidate olfactory genes. We obtained 53,892 unigenes, 16,185 of which were annotated. Based on annotations, we identified 49 unigenes related to chemoreception, including four odourant-binding proteins, three chemosensory proteins, 37 odourant receptors, two odourant ionotropic receptors and three sensory neuron membrane proteins. This is the first report on the molecular basis of the chemosensory system of C. rogenhoferi. The findings provide a basis for elucidating the molecular mechanisms of the olfactory-related behaviours of C. rogenhoferi, which would facilitate a better application of C. rogenhoferi as a biological control agent.

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 Transcriptome Analysis of Pre-Storage 1-MCP and High CO2-Treated ‘Madoka’ Peach Fruit Explains the Reduction in Chilling Injury and Improvement of Storage Period by Delaying Ripening

2021 ◽  
Vol 22 (9) ◽  
pp. 4437
Author(s):  
Han Ryul Choi ◽  
Min Jae Jeong ◽  
Min Woo Baek ◽  
Jong Hang Choi ◽  
Hee Cheol Lee ◽  
...  
Keyword(s):  
Cold Storage ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Chilling Injury ◽  
Chemical Properties ◽  
Storage Period ◽  
Differentially Expressed ◽  
Peach Fruit ◽  
High Co2 ◽  
Physico Chemical

Cold storage of peach fruit at low temperatures may induce chilling injury (CI). Pre-storage 1-MCP and high CO2 treatments were reported among the methods to ameliorate CI and reduce softening of peach fruit. However, molecular data indicating the changes associated with pre-storage 1-MCP and high CO2 treatments during cold storage of peach fruit are insufficient. In this study, a comparative analysis of the difference in gene expression and physico-chemical properties of fruit at commercial harvest vs. stored fruit for 12 days at 0 °C (cold-stored (CS), pre-storage 1-MCP+CS, and pre-storage high CO2+CS) were used to evaluate the variation among treatments. Several genes were differentially expressed in 1-MCP+CS- and CO2+CS-treated fruits as compared to CS. Moreover, the physico-chemical and sensory data indicated that 1-MCP+CS and CO2+CS suppressed CI and delayed ripening than the CS, which could lead to a longer storage period. We also identified the list of genes that were expressed commonly and exclusively in the fruit treated by 1-MCP+CS and CO2+CS and compared them to the fruit quality parameters. An attempt was also made to identify and categorize genes related to softening, physiological changes, and other ripening-related changes. Furthermore, the transcript levels of 12 selected representative genes from the differentially expressed genes (DEGs) in the transcriptome analysis were confirmed via quantitative real-time PCR (qRT-PCR). These results add information on the molecular mechanisms of the pre-storage treatments during cold storage of peach fruit. Understanding the genetic response of susceptible cultivars such as ‘Madoka’ to CI-reducing pre-storage treatments would help breeders release CI-resistant cultivars and could help postharvest technologists to develop more CI-reducing technologies.

Transcriptome Analysis Reveals Complex Molecular Mechanisms Underlying UV Tolerance of Wheat (Triticum aestivum, L.)

2018 ◽  
Vol 67 (2) ◽  
pp. 563-577 ◽  
Author(s):  
Fang Wang ◽  
Zhibin Xu ◽  
Xiaoli Fan ◽  
Qiang Zhou ◽  
Jun Cao ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Triticum Aestivum L ◽  
Uv Tolerance

scholarly journals Abstract LB-326: Full-Length mRNA transcriptome analysis of matched circulating tumor and immune cells from breast cancer subjects

2019 ◽  
Author(s):  
Naveen Ramalingam ◽  
Yifang Lee ◽  
Lukasz Szpankowski ◽  
Anne Leyrat ◽  
Brian Fowler ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Immune Cells ◽  
Transcriptome Analysis ◽  
Full Length ◽  
Mrna Transcriptome

Transcriptome analysis of scions grafted to potato rootstock for improving late blight resistance

2020 ◽  
Author(s):  
Yuexin Li ◽  
Degang Zhao
Keyword(s):  
Disease Resistance ◽  
Late Blight ◽  
Protein Kinases ◽  
Molecular Mechanisms ◽  
Late Blight Resistance ◽  
Potato Late Blight ◽  
Susceptible Variety ◽  
Resistant Variety ◽  
Blight Resistance ◽  
Expression Levels

Abstract Background: Late blight seriously threatens potato cultivation worldwide. The severe and widespread damage caused by the fungal pathogen can lead to drastic decreases in potato yield. Although grafting technology has been widely used to improve crop resistance, the effects of grafting on potato late blight resistance as well as the associated molecular mechanisms remain unclear. Therefore, we performed RNA transcriptome sequencing analysis and the late blight resistance testing of the scion when the potato late blight-resistant variety Qingshu 9 and the susceptible variety Favorita were used as the rootstock and scion, respectively, and vice versa. The objective of this study was to evaluate the influence of the rootstock on scion disease resistance and to clarify the related molecular mechanisms.Results: A Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that the expression levels of genes related to plant–pathogen interactions, plant mitogen-activated protein kinase (MAPK) signaling pathways, and plant hormone signal transduction pathways were significantly up-regulated in the scion when Qingshu 9 was used as the rootstock. These genes included late blight response genes encoding calcium-dependent protein kinases (CDPKs), chitin elicitor receptor kinases (CERKs), LRR receptor serine/threonine protein kinases (LRR-LRKs), NPR family proteins in the salicylic acid synthesis pathway, and MAPKs. When Favorita was used as the rootstock, the expression levels of the late blight response genes were not up-regulated in the Qingshu 9 scion, but the expression levels of the genes related to proline metabolism, fatty acid chain elongation, and diterpenoid biosynthesis pathways were down-regulated. Resistance results showed that self-grafting of the susceptible variety and grafting with the resistant variety as the rootstock increased the resistance of the susceptible scion to late blight. However, the resistance was stronger after grafting with the resistant variety as the rootstock. Using the susceptible variety as the rootstock decreased the late blight resistance of the resistant scion.Conclusions: Our results showed that changes to the expression of disease resistance genes in the scion after grafting are associated with late blight resistance. The results provide the basis for exploring the molecular mechanism underlying the effects of rootstocks on scion disease resistance.

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 Whole transcriptome analysis of adrenal glands from prenatal glucocorticoid programmed hypertensive rodents

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sujeenthar Tharmalingam ◽  
Sandhya Khurana ◽  
Alyssa Murray ◽  
Jeremy Lamothe ◽  
T. C. Tai
Keyword(s):  
Gene Expression ◽  
Circadian Rhythm ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Adrenal Glands ◽  
Genetic Model ◽  
Pathway Enrichment Analysis ◽  
Wistar Kyoto ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Abstract Prenatal glucocorticoid exposure is associated with the development of hypertension in adults. We have previously demonstrated that antenatal dexamethosone (DEX) administration in Wistar-Kyoto dams results in offspring with increased blood pressure coupled with elevated plasma epinephrine levels. In order to elucidate the molecular mechanisms responsible for prenatal DEX-mediated programming of hypertension, a whole-transcriptome analysis was performed on DEX programmed WKY male adrenal glands using the Rat Gene 2.0 microarray. Differential gene expression (DEG) analysis of DEX-exposed offspring compared with saline-treated controls revealed 142 significant DEGs (109 upregulated and 33 downregulated genes). DEG pathway enrichment analysis demonstrated that genes involved in circadian rhythm signaling were most robustly dysregulated. RT-qPCR analysis confirmed the increased expression of circadian genes Bmal1 and Npas2, while Per2, Per3, Cry2 and Bhlhe41 were significantly downregulated. In contrast, gene expression profiling of Spontaneously Hypertensive (SHR) rats, a genetic model of hypertension, demonstrated decreased expression of Bmal1 and Npas2, while Per1, Per2, Per3, Cry1, Cry2, Bhlhe41 and Csnk1D were all upregulated compared to naïve WKY controls. Taken together, this study establishes that glucocorticoid programmed adrenals have impaired circadian signaling and that changes in adrenal circadian rhythm may be an underlying molecular mechanism responsible for the development of hypertension.

scholarly journals Transcriptome Analysis of Watermelon Leaves Reveals Candidate Genes Responsive to Cucumber green mottle mosaic virus Infection

2019 ◽  
Vol 20 (3) ◽  
pp. 610 ◽  
Author(s):  
Yuyan Sun ◽  
Min Fan ◽  
Yanjun He
Keyword(s):  
Mosaic Virus ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Plant Hormone ◽  
Pcr Analysis ◽  
Whole Plant ◽  
Plant Pathogen Interactions ◽  
Differently Expressed Genes

Cucumber green mottle mosaic virus (CGMMV) is a member of the genus Tobamovirus, which cause diseases in cucurbits, especially watermelon. In watermelon, symptoms develop on the whole plant, including leaves, stems, peduncles, and fruit. To better understand the molecular mechanisms of watermelon early responses to CGMMV infection, a comparative transcriptome analysis of 24 h CGMMV-infected and mock-inoculated watermelon leaves was performed. A total of 1641 differently expressed genes (DEGs) were identified, with 886 DEGs upregulated and 755 DEGs downregulated after CGMMV infection. A functional analysis indicated that the DEGs were involved in photosynthesis, plant–pathogen interactions, secondary metabolism, and plant hormone signal transduction. In addition, a few transcription factor families, including WRKY, MYB, HLH, bZIP and NAC, were responsive to the CGMMV-induced stress. To confirm the high-throughput sequencing results, 15 DEGs were validated by qRT-PCR analysis. The results provide insights into the identification of candidate genes or pathways involved in the responses of watermelon leaves to CGMMV infection.

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