Third-generation sequencing and metabolome analysis reveal candidate genes and metabolites with altered levels in albino jackfruit seedlings

Abstract Background Most plants rely on photosynthesis; therefore, albinism in plants with leaves that are white instead of green causes slow growth, dwarfing, and even death. Although albinism has been characterized in annual model plants, little is known about albino trees. Jackfruit (Artocarpus heterophyllus) is an important tropical fruit tree species. To gain insight into the mechanisms underlying the differential growth and development between albino jackfruit mutants and green seedlings, we analyzed root, stem, and leaf tissues by combining PacBio single-molecule real-time (SMRT) sequencing, high-throughput RNA-sequencing (RNA-seq), and metabolomic analysis. Results We identified 8,202 differentially expressed genes (DEGs), including 225 genes encoding transcription factors (TFs), from 82,572 full-length transcripts. We also identified 298 significantly changed metabolites (SCMs) in albino A. heterophyllus seedlings from a set of 692 metabolites in A. heterophyllus seedlings. Pathway analysis revealed that these DEGs were highly enriched in metabolic pathways such as ‘photosynthesis’, ‘carbon fixation in photosynthetic organisms’, ‘glycolysis/gluconeogenesis’, and ‘TCA cycle’. Analysis of the metabolites revealed 76 SCMs associated with metabolic pathways in the albino mutants, including L-aspartic acid, citric acid, succinic acid, and fumaric acid. We selected 225 differentially expressed TF genes, 333 differentially expressed metabolic pathway genes, and 76 SCMs to construct two correlation networks. Analysis of the TF–DEG network suggested that basic helix-loop-helix (bHLH) and MYB-related TFs regulate the expression of genes involved in carbon fixation and energy metabolism to affect light responses or photomorphogenesis and normal growth. Further analysis of the DEG–SCM correlation network and the photosynthetic carbon fixation pathway suggested that NAD-ME2 (encoding a malic enzyme) and L-aspartic acid jointly inhibit carbon fixation in the albino mutants, resulting in reduced photosynthetic efficiency and inhibited plant growth. Conclusions Our preliminarily screening identified candidate genes and metabolites specifically affected in albino A. heterophyllus seedlings, laying the foundation for further study of the regulatory mechanism of carbon fixation during photosynthesis and energy metabolism. In addition, our findings elucidate the way genes and metabolites respond in albino trees.

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Transcriptomic responses of Microcystis aeruginosa under electromagnetic radiation exposure

Scientific Reports ◽

10.1038/s41598-020-80830-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Chao Tang ◽

Ziyan Zhang ◽

Shen Tian ◽

Peng Cai

Keyword(s):

Energy Metabolism ◽

Electromagnetic Radiation ◽

Differentially Expressed Genes ◽

Microcystis Aeruginosa ◽

Carbon Fixation ◽

Biological Effects ◽

Differentially Expressed ◽

Ecological Environment ◽

Inhibit Protein Synthesis ◽

Potential Threat

AbstractElectromagnetic radiation is an important environmental factor. It has a potential threat to public health and ecological environment. However, the mechanism by which electromagnetic radiation exerts these biological effects remains unclear. In this study, the effect of Microcystis aeruginosa under electromagnetic radiation (1.8 GHz, 40 V/m) was studied by using transcriptomics. A total of 306 differentially expressed genes, including 121 upregulated and 185 downregulated genes, were obtained in this study. The differentially expressed genes were significantly enriched in the ribosome, oxidative phosphorylation and carbon fixation pathways, indicating that electromagnetic radiation may inhibit protein synthesis and affect cyanobacterial energy metabolism and photosynthesis. The total ATP synthase activity and ATP content significantly increased, whereas H+K+-ATPase activity showed no significant changes. Our results suggest that the energy metabolism pathway may respond positively to electromagnetic radiation. In the future, systematic studies on the effects of electromagnetic radiation based on different intensities, frequencies, and exposure times are warranted; to deeply understand and reveal the target and mechanism of action of electromagnetic exposure on organisms.

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Serum Biomarker Identification by Mass Spectrometry in Acute Aortic Dissection

Cellular Physiology and Biochemistry ◽

10.1159/000485954 ◽

2017 ◽

Vol 44 (6) ◽

pp. 2147-2157 ◽

Cited By ~ 6

Author(s):

Yong Ren ◽

Qizhu Tang ◽

Wenwei Liu ◽

Yongqian Tang ◽

Rui Zhu ◽

...

Keyword(s):

Mass Spectrometry ◽

Aortic Dissection ◽

Peripheral Blood ◽

Metabolic Pathways ◽

Healthy Subjects ◽

Ether Lipid ◽

Intramural Hematoma ◽

Differentially Expressed ◽

Metabolome Analysis ◽

Hypertensive Patients

Background/Aims: Aortic dissection (AD) is also known as intramural hematoma. This study aimed to screen peripheral blood biomarkers of small molecule metabolites for AD using high-performance liquid chromatography-mass spectrometry (HPLC-MS). Methods: Sera from 25 healthy subjects, 25 patients with well-established AD, and 25 patients with well-established hypertension were investigated by HPLC-MS to detect metabolites, screen differentially expressed metabolites, and analyze metabolic pathways. Results: Twenty-six and four metabolites were significantly up- and down-regulated in the hypertensive patients compared with the healthy subjects; 165 metabolites were significantly up-regulated and 109 significantly down-regulated in the AD patients compared with the hypertensive patients. Of these metabolites, 35 were up-regulated and 105 down-regulated only in AD patients. The metabolites that were differentially expressed in AD are mainly involved in tryptophan, histidine, glycerophospholipid, ether lipid, and choline metabolic pathways. As AD alters the peripheral blood metabolome, analysis of peripheral blood metabolites can be used in auxiliary diagnosis of AD. Conclusion: Eight metabolites are potential biomarkers for AD, 3 of which were differentially expressed and can be used for auxiliary diagnosis of AD and evaluation of treatment effectiveness.

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Single-Molecule Real-Time and Illumina-Based RNA Sequencing Data Identified Vernalization-Responsive Candidate Genes in Faba Bean (Vicia faba L.)

Frontiers in Genetics ◽

10.3389/fgene.2021.656137 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xingxing Yuan ◽

Qiong Wang ◽

Bin Yan ◽

Jiong Zhang ◽

Chenchen Xue ◽

...

Keyword(s):

Real Time ◽

Candidate Genes ◽

Vicia Faba ◽

Single Molecule ◽

Faba Bean ◽

Molecular Mechanisms ◽

Ectopic Expression ◽

Full Length ◽

Differentially Expressed ◽

Sequencing Data

Faba bean (Vicia faba L.) is one of the most widely grown cool season legume crops in the world. Winter faba bean normally has a vernalization requirement, which promotes an earlier flowering and pod setting than unvernalized plants. However, the molecular mechanisms of vernalization in faba bean are largely unknown. Discovering vernalization-related candidate genes is of great importance for faba bean breeding. In this study, the whole transcriptome of faba bean buds was profiled by using next-generation sequencing (NGS) and single-molecule, real-time (SMRT) full-length transcriptome sequencing technology. A total of 29,203 high-quality non-redundant transcripts, 21,098 complete coding sequences (CDS), 1,045 long non-coding RNAs (lncRNAs), and 12,939 simple sequence repeats (SSRs) were identified. Furthermore, 4,044 differentially expressed genes (DEGs) were identified through pairwise comparisons. By Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, these differentially expressed transcripts were found to be enriched in binding and transcription factor activity, electron carrier activity, rhythmic process, and receptor activity. Finally, 50 putative vernalization-related genes that played important roles in the vernalization of faba bean were identified; we also found that the levels of vernalization-responsive transcripts showed significantly higher expression levels in cold-treated buds. The expression of VfSOC1, one of the candidate genes, was sensitive to vernalization. Ectopic expression of VfSOC1 in Arabidopsis brought earlier flowering. In conclusion, the abundant vernalization-related transcripts identified in this study will provide a basis for future researches on the vernalization and faba bean breeding and established a reference full-length transcriptome for future studies on faba bean.

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Integrated Analysis of Metabolome and Transcriptome Reveals Insights for Cold Tolerance in Rapeseed (Brassica napus L.)

Frontiers in Plant Science ◽

10.3389/fpls.2021.721681 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ali Raza ◽

Wei Su ◽

Muhammad Azhar Hussain ◽

Sundas Saher Mehmood ◽

Xuekun Zhang ◽

...

Keyword(s):

Brassica Napus ◽

Candidate Genes ◽

Differentially Expressed Genes ◽

Crop Improvement ◽

Functional Enrichment ◽

Differentially Expressed ◽

Integrated Analysis ◽

Oilseed Crop ◽

Metabolome Analysis ◽

Tolerance Mechanisms

Rapeseed (Brassica napus L.) is an important oilseed crop in the world. Its productivity is significantly influenced by numerous abiotic stresses, including cold stress (CS). Consequently, enhancement in CS tolerance is becoming an important area for agricultural investigation and crop improvement. Therefore, the current study aimed to identify the stress-responsive genes, metabolites, and metabolic pathways based on a combined transcriptome and metabolome analysis to understand the CS responses and tolerance mechanisms in the cold-tolerant (C18) and cold-sensitive (C6) rapeseed varieties. Based on the metabolome analysis, 31 differentially accumulated metabolites (DAMs) were identified between different comparisons of both varieties at the same time points. From the transcriptome analysis, 2,845, 3,358, and 2,819 differentially expressed genes (DEGs) were detected from the comparison of C6-0 vs. C18-0, C6-1 vs. C18-1, and C6-7 vs. C18-7. By combining the transcriptome and metabolome data sets, we found that numerous DAMs were strongly correlated with several differentially expressed genes (DEGs). A functional enrichment analysis of the DAMs and the correlated DEGs specified that most DEGs and DAMs were mainly enriched in diverse carbohydrates and amino acid metabolisms. Among them, starch and sucrose metabolism and phenylalanine metabolism were significantly enriched and played a vital role in the CS adaption of rapeseed. Six candidate genes were selected from the two pathways for controlling the adaption to low temperature. In a further validation, the T-DNA insertion mutants of their Arabidopsis homologous, including 4cl3, cel5, fruct4, ugp1, axs1, and bam2/9, were characterized and six lines differed significantly in levels of freezing tolerance. The outcome of the current study provided new prospects for the understanding of the molecular basis of CS responses and tolerance mechanisms in rapeseed and present a set of candidate genes for use in improving CS adaptability in the same plant.

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Transcriptional identification of differentially expressed genes during the prepupal–pupal transition in the oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

Bulletin of Entomological Research ◽

10.1017/s0007485321000171 ◽

2021 ◽

pp. 1-14

Author(s):

Peirong Li ◽

Xinru Li ◽

Wei Wang ◽

Xiaoling Tan ◽

Xiaoqi Wang ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Metabolic Pathways ◽

Developmental Stages ◽

Kegg Pathway ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Mythimna Separata ◽

Kegg Pathway Analysis ◽

Oriental Armyworm ◽

Lepidoptera Noctuidae

Abstract The oriental armyworm, Mythimna separata (Walker) is a serious pest of agriculture that does particular damage to Gramineae crops in Asia, Europe, and Oceania. Metamorphosis is a key developmental stage in insects, although the genes underlying the metamorphic transition in M. separata remain largely unknown. Here, we sequenced the transcriptomes of five stages; mature larvae (ML), wandering (W), and pupation (1, 5, and 10 days after pupation, designated P1, P5, and P10) to identify transition-associated genes. Four libraries were generated, with 22,884, 23,534, 26,643, and 33,238 differentially expressed genes (DEGs) for the ML-vs-W, W-vs-P1, P1-vs-P5, and P5-vs-P10, respectively. Gene ontology enrichment analysis of DEGs showed that genes regulating the biosynthesis of the membrane and integral components of the membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs were enriched in the metabolic pathways. Of these DEGs, thirty CP, seventeen 20E, and seven JH genes were differentially expressed across the developmental stages. For transcriptome validation, ten CP, 20E, and JH-related genes were selected and verified by real-time PCR quantitative. Collectively, our results provided a basis for further studies of the molecular mechanism of metamorphosis in M. separata.

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Physiological and Proteomic Responses of Pitaya to PEG-Induced Drought Stress

Agriculture ◽

10.3390/agriculture11070632 ◽

2021 ◽

Vol 11 (7) ◽

pp. 632

Author(s):

Aihua Wang ◽

Chao Ma ◽

Hongye Ma ◽

Zhilang Qiu ◽

Xiaopeng Wen

Keyword(s):

Drought Stress ◽

Energy Metabolism ◽

Metabolic Pathways ◽

Treatment Time ◽

Soluble Sugar ◽

Antioxidant Systems ◽

Antioxidant Enzyme Activities ◽

Proteomic Data ◽

Proteome Profile ◽

Proteomic Responses

Pitaya (Hylocereus polyrhizus L.) is highly tolerant to drought stress. Elucidating the response mechanism of pitaya to drought will substantially contribute to improving crop drought tolerance. In the present study, the physiological and proteomic responses of the pitaya cultivar ‘Zihonglong’ were compared between control seedlings and seedlings exposed to drought stress (−4.9 MPa) induced by polyethylene glycol for 7 days. Drought stress obviously enhanced osmolyte accumulation, lipid peroxidation, and antioxidant enzyme activities. Proteomic data revealed drought stress activated several pathways in pitaya, including carbohydrate and energy metabolism at two drought stress treatment time-points (6 h and 3 days). Other metabolic pathways, including those related to aspartate, glutamate, glutathione, and secondary metabolites, were induced more at 3 days than at 6 h, whereas photosynthesis and arginine metabolism were induced exclusively at 6 h. Overall, protein expression changes were consistent with the physiological responses, although there were some differences in the timing. The increases in soluble sugar contents mainly resulted from the degradation and transformation of insoluble carbohydrates. Differentially accumulated proteins in amino acid metabolism may be important for the conversion and accumulation of amino acids. GSH and AsA metabolism and secondary metabolism may play important roles in pitaya as enzymatic and nonenzymatic antioxidant systems. The enhanced carbohydrate and energy metabolism may provide the energy necessary for initiating the above metabolic pathways. The current study provided the first proteome profile of this species exposed to drought stress, and may clarify the mechanisms underlying the considerable tolerance of pitaya to drought stress.

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The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality

BMC Plant Biology ◽

10.1186/s12870-021-02858-1 ◽

2021 ◽

Vol 21 (1) ◽

Cited By ~ 1

Author(s):

Ian S. E. Bally ◽

◽

Aureliano Bombarely ◽

Alan H. Chambers ◽

Yuval Cohen ◽

...

Keyword(s):

Candidate Genes ◽

Fruit Quality ◽

De Novo ◽

Mapping Population ◽

Mangifera Indica ◽

Consensus Sequence ◽

Fruit Size ◽

Hybrid Population ◽

High Molecular Weight Dna ◽

Tropical Fruit

Abstract Background Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency. Results This study sequenced, de novo assembled, analyzed, and annotated the genome of the monoembryonic mango cultivar ‘Tommy Atkins’. The draft genome sequence was generated using NRGene de-novo Magic on high molecular weight DNA of ‘Tommy Atkins’, supplemented by 10X Genomics long read sequencing to improve the initial assembly. A hybrid population between ‘Tommy Atkins’ x ‘Kensington Pride’ was used to generate phased haplotype chromosomes and a highly resolved phased SNP map. The final ‘Tommy Atkins’ genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango and included ~ 86% of the ~ 439 Mb haploid mango genome. Skim sequencing identified ~ 3.3 M SNPs using the ‘Tommy Atkins’ x ‘Kensington Pride’ mapping population. Repeat masking identified 26,616 genes with a median length of 3348 bp. A whole genome duplication analysis revealed an ancestral 65 MYA polyploidization event shared with Anacardium occidentale. Two regions, one on LG4 and one on LG7 containing 28 candidate genes, were associated with the commercially important fruit size characteristic in the mapping population. Conclusions The availability of the complete ‘Tommy Atkins’ mango genome will aid global initiatives to study mango genetics.

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Metabolomic profiling of anaerobic and aerobic energy metabolic pathways in chronic obstructive pulmonary disease

Experimental Biology and Medicine ◽

10.1177/15353702211008808 ◽

2021 ◽

pp. 153537022110088

Author(s):

Mingshan Xue ◽

Yifeng Zeng ◽

Runpei Lin ◽

Hui-Qi Qu ◽

Teng Zhang ◽

...

Keyword(s):

Chronic Obstructive Pulmonary Disease ◽

Energy Metabolism ◽

Pulmonary Disease ◽

Metabolic Pathways ◽

Energy Supply ◽

Stable Phase ◽

Chronic Obstructive ◽

Obstructive Pulmonary Disease ◽

Copd Patients ◽

Anaerobic Energy

While there is no cure for chronic obstructive pulmonary disease (COPD), its progressive nature and the formidable challenge to manage its symptoms warrant a more extensive study of the pathogenesis and related mechanisms. A new emphasis on COPD study is the change of energy metabolism. For the first time, this study investigated the anaerobic and aerobic energy metabolic pathways in COPD using the metabolomic approach. Metabolomic analysis was used to investigate energy metabolites in 140 COPD patients. The significance of energy metabolism in COPD was comprehensively explored by the Global Initiative for Chronic Obstructive Lung Disease–GOLD grading, acute exacerbation vs. stable phase (either clinical stability or four-week stable phase), age group, smoking index, lung function, and COPD Assessment Test (CAT) score. Through comprehensive evaluation, we found that COPD patients have a significant imbalance in the aerobic and anaerobic energy metabolisms in resting state, and a high tendency of anaerobic energy supply mechanism that correlates positively with disease progression. This study highlighted the significance of anaerobic and low-efficiency energy supply pathways in lung injury and linked it to the energy-inflammation-lung ventilatory function and the motion limitation mechanism in COPD patients, which implies a novel therapeutic direction for this devastating disease.

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4 Molecularly guided multiplexed digital spatial analysis reveals differential gene expression profiles in the WNT-β-catenin pathway between melanoma and prostate tumors

Journal for ImmunoTherapy of Cancer ◽

10.1136/jitc-2020-sitc2020.0004 ◽

2020 ◽

Vol 8 (Suppl 3) ◽

pp. A4-A4

Author(s):

Anushka Dikshit ◽

Dan Zollinger ◽

Karen Nguyen ◽

Jill McKay-Fleisch ◽

Kit Fuhrman ◽

...

Keyword(s):

Gene Expression ◽

Single Cell ◽

Single Molecule ◽

Spatial Information ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Fluorescence Assay ◽

Differentially Expressed ◽

Tumor Type ◽

Prostate Tumors

BackgroundThe canonical WNT-β-catenin signaling pathway is vital for development and tissue homeostasis but becomes strongly tumorigenic when dysregulated. and alter the transcriptional signature of a cell to promote malignant transformation. However, thorough characterization of these transcriptomic signatures has been challenging because traditional methods lack either spatial information, multiplexing, or sensitivity/specificity. To overcome these challenges, we developed a novel workflow combining the single molecule and single cell visualization capabilities of the RNAscope in situ hybridization (ISH) assay with the highly multiplexed spatial profiling capabilities of the GeoMx™ Digital Spatial Profiler (DSP) RNA assays. Using these methods, we sought to spatially profile and compare gene expression signatures of tumor niches with high and low CTNNB1 expression.MethodsAfter screening 120 tumor cores from multiple tumors for CTNNB1 expression by the RNAscope assay, we identified melanoma as the tumor type with the highest CTNNB1 expression while prostate tumors had the lowest expression. Using the RNAscope Multiplex Fluorescence assay we selected regions of high CTNNB1 expression within 3 melanoma tumors as well as regions with low CTNNB1 expression within 3 prostate tumors. These selected regions of interest (ROIs) were then transcriptionally profiled using the GeoMx DSP RNA assay for a set of 78 genes relevant in immuno-oncology. Target genes that were differentially expressed were further visualized and spatially assessed using the RNAscope Multiplex Fluorescence assay to confirm GeoMx DSP data with single cell resolution.ResultsThe GeoMx DSP analysis comparing the melanoma and prostate tumors revealed that they had significantly different gene expression profiles and many of these genes showed concordance with CTNNB1 expression. Furthermore, immunoregulatory targets such as ICOSLG, CTLA4, PDCD1 and ARG1, also demonstrated significant correlation with CTNNB1 expression. On validating selected targets using the RNAscope assay, we could distinctly visualize that they were not only highly expressed in melanoma compared to the prostate tumor, but their expression levels changed proportionally to that of CTNNB1 within the same tumors suggesting that these differentially expressed genes may be regulated by the WNT-β-catenin pathway.ConclusionsIn summary, by combining the RNAscope ISH assay and the GeoMx DSP RNA assay into one joint workflow we transcriptionally profiled regions of high and low CTNNB1 expression within melanoma and prostate tumors and identified genes potentially regulated by the WNT- β-catenin pathway. This novel workflow can be fully automated and is well suited for interrogating the tumor and stroma and their interactions.GeoMx Assays are for RESEARCH ONLY, not for diagnostics.

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Identifying Candidate Genes for Hypoxia Adaptation of Tibet Chicken Embryos by Selection Signature Analyses and RNA Sequencing

Genes ◽

10.3390/genes11070823 ◽

2020 ◽

Vol 11 (7) ◽

pp. 823

Author(s):

Xiayi Liu ◽

Xiaochen Wang ◽

Jing Liu ◽

Xiangyu Wang ◽

Haigang Bao

Keyword(s):

Candidate Genes ◽

Rna Sequencing ◽

Differentially Expressed Genes ◽

Gallus Gallus ◽

Differentially Expressed ◽

Tibet Plateau ◽

Embryonic Liver ◽

Selection Signature ◽

Chicken Embryos ◽

Hypoxia Adaptation

The Tibet chicken (Gallus gallus) lives on the Qinghai–Tibet Plateau and adapts to the hypoxic environment very well. The objectives of this study was to obtain candidate genes associated with hypoxia adaptation in the Tibet chicken embryos. In the present study, we used the fixation index (Fst) and cross population extended haplotype homozygosity (XPEHH) statistical methods to detect signatures of positive selection of the Tibet chicken, and analyzed the RNA sequencing data from the embryonic liver and heart with HISAT, StringTie and Ballgown for differentially expressed genes between the Tibet chicken and White leghorn (Gallus gallus, a kind of lowland chicken) embryos hatched under hypoxia condition. Genes which were screened out by both selection signature analysis and RNA sequencing analysis could be regarded as candidate genes for hypoxia adaptation of chicken embryos. We screened out 1772 genes by XPEHH and 601 genes by Fst, and obtained 384 and 353 differentially expressed genes in embryonic liver and heart, respectively. Among these genes, 89 genes were considered as candidate genes for hypoxia adaptation in chicken embryos. ARNT, AHR, GSTK1 and FGFR1 could be considered the most important candidate genes. Our findings provide references to elucidate the molecular mechanism of hypoxia adaptation in Tibet chicken embryos.

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