scholarly journals Integrated analysis of full-length transcriptome and secondary metabolism reveals novel regulation in Paulownia fortunei infected with phytoplasma

2019 ◽  
Author(s):  
Xiaogai Zhao ◽  
Xiaoqiao Zhai ◽  
Zhe Wang ◽  
Yabing Cao ◽  
Zhenli Zhao ◽  
...  
Keyword(s):  
Single Molecule ◽  
High Performance ◽  
Molecular Mechanisms ◽  
Economic Losses ◽  
Integrated Analysis ◽  
Liquid Chromatography Mass Spectrometry ◽  
Smrt Sequencing ◽  
Gene Annotations ◽  
Annotation Information ◽  
Paulownia Fortunei

Abstract Background: Paulownia witches' broom (PaWB) is a devastating disease caused by phytoplasma, which can lead to considerable economic losses. Previous studies have shown that 60 mg•L-1 methyl methane sulfonate (MMS) can restore infected Paulownia seedlings to healthy one. To improve the understanding of PaWB, we used single molecule real time (SMRT) sequencing, which can provide long sequences that can be effectively used to identify gene alternative splicing, obtain novel genes, improve gene annotations and comprehensive analysis of the metabolome. Results: Here, the first integrated analysis SMRT sequencing, the Illumina platforms, and high-performance liquid chromatography-mass spectrometry (HPLC-MS) to analyze changes in transcripts and metabolites in Paulownia fortunei. A total of 140,528 non redundant transcripts were identified, which supported 6,209 of novel gene loci that can enrich 70,223 annotation information of Paulownia fortunei （P. fortunei）genome. A total of 5,606 transcripts, 46 lncRNAs, 83 fusion transcripts, 597 transcription factors, and 57 metabolites were related indirectly or directly to PaWB. Subsequent analysis of the transcriptome and metabolome found trans-cinnamate 4-monooxygenase, caffeoyl-CoA-O methyltransferase, ferulic acid and peroxidase were up-regulated in Paulownia fortunei infected with phytoplasma. They were involved in flavonoid, phenylpropane and salicylic acid metabolism, which might be related to Paulownia-phytoplasma interaction. Conclusions: Our results will enrich the understanding of molecular mechanisms of PaWB. This study provides a foundation for better understanding the changes in gene expression, metabolites, and morphology of Paulownia fortunei with PaWB.

scholarly journals Genome Sequencing of Cladobotryum protrusum Provides Insights into the Evolution and Pathogenic Mechanisms of the Cobweb Disease Pathogen on Cultivated Mushroom

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 124 ◽  
Author(s):  
Frederick Sossah ◽  
Zhenghui Liu ◽  
Chentao Yang ◽  
Benjamin Okorley ◽  
Lei Sun ◽  
...  
Keyword(s):  
Single Molecule ◽  
Molecular Mechanisms ◽  
Divergence Time ◽  
Edible Mushrooms ◽  
Economic Losses ◽  
Phylogenomic Analysis ◽  
Evolutionary Divergence ◽  
Cytochrome P450 Enzymes ◽  
Sequencing Platform ◽  
Cobweb Disease

Cladobotryum protrusum is one of the mycoparasites that cause cobweb disease on cultivated edible mushrooms. However, the molecular mechanisms of evolution and pathogenesis of C. protrusum on mushrooms are largely unknown. Here, we report a high-quality genome sequence of C. protrusum using the single-molecule, real-time sequencing platform of PacBio and perform a comparative analysis with closely related fungi in the family Hypocreaceae. The C. protrusum genome, the first complete genome to be sequenced in the genus Cladobotryum, is 39.09 Mb long, with an N50 of 4.97 Mb, encoding 11,003 proteins. The phylogenomic analysis confirmed its inclusion in Hypocreaceae, with its evolutionary divergence time estimated to be ~170.1 million years ago. The genome encodes a large and diverse set of genes involved in secreted peptidases, carbohydrate-active enzymes, cytochrome P450 enzymes, pathogen–host interactions, mycotoxins, and pigments. Moreover, C. protrusum harbors arrays of genes with the potential to produce bioactive secondary metabolites and stress response-related proteins that are significant for adaptation to hostile environments. Knowledge of the genome will foster a better understanding of the biology of C. protrusum and mycoparasitism in general, as well as help with the development of effective disease control strategies to minimize economic losses from cobweb disease in cultivated edible mushrooms.

scholarly journals Identification of Antimicrobial Peptide Genes in Black Rockfish Sebastes schlegelii and Their Responsive Mechanisms to Edwardsiella tarda Infection

Biology ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1015
Author(s):  
Min Zhang ◽  
Min Cao ◽  
Yunji Xiu ◽  
Qiang Fu ◽  
Ning Yang ◽  
...  
Keyword(s):  
Antimicrobial Peptide ◽  
Single Molecule ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Amino Acid Sequences ◽  
Edwardsiella Tarda ◽  
Economic Losses ◽  
Dominant Type ◽  
Black Rockfish ◽  
Sebastes Schlegelii

The black rockfish, Sebastes schlegelii, is a typical viviparous teleost, which belongs to the family Scorpaenidae. Due to its high economic and ecological values, S. schlegelii has been widely cultured in East Asian countries. With the enlargement of cultivation scale, bacterial and viral diseases have become the main threats to the farming industry of S. schlegelii, which have resulted in significant economic losses. In this study, Illumina shotgun sequencing, single-molecule real-time (SMRT) sequencing, 10x genomics and high-throughput chromosome conformation capture (Hi-C) technologies were collectively applied to assemble the genome of S. schlegelii. Then, we identified the antimicrobial peptide genes (AMPs) in the S. schlegelii genome. In total, 214 AMPs were identified in the S. schlegelii genome, which can be divided into 33 classes according to the annotation and cataloging of the Antimicrobial Peptides Database (APD3). Among these AMPs, thrombin-derived C-terminal peptide (TCP) was the dominant type, followed by RegIIIgamma and chemokine. The amino acid sequences of the TCP, cgUbiquitin, RegIIIalpha, RegIIIgamma, chemokine shared 32.55%, 42.63%, 29.87%, 28.09%, and 32.15% similarities among the same type in S. schlegelii. Meanwhile, the expression patterns of these AMPs in nine healthy tissues and at different infection time points in intestine were investigated. The results showed that the numbers and types of AMPs that responded to Edwardsiella tarda infection gradually increased as the infection progressed. In addition, we analyzed the phylogenetic relationships of hepcidins in teleost. The identification of AMPs based on the whole genome could provide a comprehensive database of potential AMPs, and benefit for the understanding of the molecular mechanisms of immune responses to E. tarda infection in S. schlegelii. This would further offer insights into an accurate and effective design and development of AMP for aquaculture therapy in the future.

scholarly journals Transcriptome analysis in the shell gland of laying hens affecting eggshell qualities

2020 ◽  
Author(s):  
Xinyue Yang ◽  
Fuping Zhao ◽  
Qiqi Han ◽  
Yuanyang Dong ◽  
Jiaqi Lei ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Laying Hens ◽  
Economic Losses ◽  
Integrated Analysis ◽  
Shell Gland ◽  
Sequencing Data ◽  
Physical Damage ◽  
Eggshell Quality ◽  
Dietary Nutrient ◽  
Gland Development

Abstract Background Eggshell plays an important role in protecting against physical damage and microorganic invasion. It is subject to quality loss with increasing hen age, and fragile eggshells result in huge economic losses to the poultry industry. Therefore, improving eggshell quality is particularly important. However, little is known about the potential molecular mechanisms regulating eggshell quality in chickens. Methods In this study, we aimed to compare differential expression of long non-coding RNAs (lncRNAs) and mRNAs between old and young laying hens to identify related candidate genes for chicken shell gland development by the method of high-throughput RNA sequencing (RNA-seq). Results In total, we detected 176 and 383 differentially expressed (DE) lncRNAs and mRNAs, respectively. Moreover, functional annotation analysis based on the Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases revealed that DE-lncRNAs and DE-mRNAs were significantly enriched in “phosphate-containing compound metabolic process”, “mitochondrial proton-transporting ATP synthase complex”, “inorganic anion transport”, and other terms related to eggshell calcification and cuticularization. Through integrated analysis, we found that some important genes such as FGF14, COL25A1, GPX8, and GRXCR1 and their corresponding lncRNAs were expressed differentially between two groups, and the results of quantitative real-time polymerase chain reaction (qPCR) among these genes were also in excellent agreement with the sequencing data. In addition, our research indicates that FGF14, COL25A1, GPX8, and the members of the SLC family may be key genes that affect eggshell quality in hens. Conclusions This study provides a catalog of lncRNAs and mRNAs of the laying hen eggshell gland and will contribute to a fuller understanding of the molecular mechanisms of the function of the shell gland in poultry. Our findings will provide a valuable reference for the development of breeding programs aimed at breeding excellent poultry with high eggshell quality or regulating dietary nutrient levels to improve eggshell quality.

scholarly journals Integrative Physiological, Transcriptional, and Metabolic Analyses Provide Insights Into Response Mechanisms of Prunus persica to Autotoxicity Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Wanqi Shen ◽  
Chunfa Zeng ◽  
He Zhang ◽  
Kaijie Zhu ◽  
Hao He ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Prunus Persica ◽  
Mineral Metabolism ◽  
Critical Factor ◽  
Metabolic Reprogramming ◽  
Economic Losses ◽  
Integrated Analysis ◽  
Land Utilization ◽  
Chlorophyll Contents ◽  
Replant Problem

Autotoxicity is known as a critical factor in replanting problem that reduces land utilization and creates economic losses. Benzoic acid (BA) is identified as a major autotoxin in peach replant problem, and causes stunted seedling growth or even death. However, the physiological and molecular mechanisms of peach response to BA stress remain elusive. Here, we comprehensively studied the morphophysiological, transcriptional, and metabolic responses of peach plants to BA toxicity. Results showed that BA stress inhibited peach seedlings growth, decreased chlorophyll contents and fluorescence levels, as well as disturbed mineral metabolism. The contents of hydrogen peroxide, superoxide anion, and malondialdehyde, as well as the total antioxidant capacity, were significantly increased under BA stress. A total of 6,319 differentially expressed genes (DEGs) were identified after BA stress, of which the DEGs related to photosynthesis, redox, and ion metabolism were greatly changed; meanwhile, numerous stress-responsive genes (HSPs, GSTs, GR, and ABC transporters) and transcription factors (MYB, AP2/ERF, NAC, bHLH, and WRKY) were noticeably altered under BA stress. BA induced metabolic reprogramming, and 74 differentially accumulated metabolites, including amino acids and derivatives, fatty acids, organic acids, sugars, and sugar alcohols, were identified in BA-stressed roots. Furthermore, an integrated analysis of genes and metabolites indicated that most of the co-mapped KEGG pathways were enriched in amino acid and carbohydrate metabolism, which implied a disturbed carbon and nitrogen metabolism after BA stress. The findings would be insightful in elucidating the mechanisms of plant response to autotoxicity stress, and help guide crops in alleviating replant problem.

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