scholarly journals Integrated Transcriptome and Metabolome Analysis Reveals Key Metabolites Involved in Camellia oleifera Defense against Anthracnose

2022 ◽  
Vol 23 (1) ◽  
pp. 536
Author(s):  
Chaochen Yang ◽  
Pengfei Wu ◽  
Xiaohua Yao ◽  
Yu Sheng ◽  
Chengcai Zhang ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Enrichment Analysis ◽  
Isoquinoline Alkaloid ◽  
Flavonoid Biosynthesis ◽  
Growth And Yield ◽  
Camellia Oleifera ◽  
Metabolome Analysis ◽  
Resistant Varieties ◽  
Phenylpropanoid Biosynthesis ◽  
Tyrosine Metabolism

Camellia oleifera (Ca. oleifera) is a woody tree species cultivated for the production of edible oil from its seed. The growth and yield of tea-oil trees are severely affected by anthracnose (caused by Colletotrichum gloeosporioides). In this study, the transcriptomic and metabolomic analyses were performed to detect the key transcripts and metabolites associated with differences in the susceptibility between anthracnose-resistant (ChangLin150) and susceptible (ChangLin102) varieties of Ca. oleifera. In total, 5001 differentially expressed genes (DEGs) were obtained, of which 479 DEGs were common between the susceptible and resistant varieties and further analyzed. KEGG enrichment analysis showed that these DEGs were significantly enriched in tyrosine metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis and isoquinoline alkaloid biosynthesis pathways. Furthermore, 68 differentially accumulated metabolites (DAMs) were detected, including flavonoids, such as epicatechin, phenethyl caffeate and procyanidin B2. Comparison of the DEGs and DAMs revealed that epicatechin, procyanidin B2 and arachidonic acid (peroxide free) are potentially important. The expression patterns of genes involved in flavonoid biosynthesis were confirmed by qRT-PCR. These results suggested that flavonoid biosynthesis might play an important role in the fight against anthracnose. This study provides valuable molecular information about the response of Ca. oleifera to Co. gloeosporioides infection and will aid the selection of resistant varieties using marker-assisted breeding.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2019 ◽  
Author(s):  
lin fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis ◽  
Mature Seeds

Abstract Abstract Backgrounds Paphiopedilum is an important genus of orchid family (Orchidaceae) with high horticultural value. The wild populations are under the threat of extinction because of over collection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts the germplasm resources protection and commercial production. The germination inhibition factors are largely unknown. Results In this study, we found large amounts of non-methylated lignin were accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. We then further compared the transcriptome profiles of P. armeniacum seed at different development stages to explore molecular clues for the non-methylated lignin synthesis. KEGG enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism as the seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathways displayed different expression patterns during the lignification process. PAL, 4CL, HCT and CSE were up-regulated to accelerate the C and H lignin accumulation. The expression of CCoAOMT, F5H and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes among seeds and vegetative tissues. Conclusions This work demonstrated the plasticity of natural lignin polymer assembly in seed, and provided a better understanding of the molecular mechanism of seed-specific lignification process.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2020 ◽  
Author(s):  
Lin Fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis ◽  
Mature Seeds

Abstract Backgrounds: Paphiopedilum is an important genus of orchid family (Orchidaceae) with high horticultural value. The wild populations are under the threat of extinction because of over collection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts the germplasm resources protection and commercial production. The germination inhibition factors are largely unknown.Results: In this study, we found large amounts of non-methylated lignin were accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. We then further compared the transcriptome profiles of P. armeniacum seed at different development stages to explore molecular clues for the non-methylated lignin synthesis. KEGG enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism as the seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathways displayed different expression patterns during the lignification process. PAL, 4CL, HCT and CSE were up-regulated to accelerate the C and H lignin accumulation. The expression of CCoAOMT, F5H and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes among seeds and vegetative tissues. Conclusions: This work demonstrated the plasticity of natural lignin polymer assembly in seed, and provided a better understanding of the molecular mechanism of seed-specific lignification process.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2020 ◽  
Author(s):  
lin fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Germplasm Conservation ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis

Abstract Backgrounds: Paphiopedilum is an important genus of the orchid family Orchidaceae and has high horticultural value. The wild populations are under threat of extinction because of overcollection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts their germplasm conservation and commercial production. The factors inhibiting germination are largely unknown.Results: In this study, large amounts of non-methylated lignin accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. The transcriptome profiles of P. armeniacum seed at different development stages were compared to explore the molecular clues for non-methylated lignin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism during seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathway displayed different expression patterns during the lignification process. PAL, 4CL, HCT, and CSE upregulation was associated with C and H lignin accumulation. The expression of CCoAOMT, F5H, and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes in seeds and vegetative tissues. Conclusions: This work demonstrated the plasticity of natural lignin polymer assembly in seed and provided a better understanding of the molecular mechanism of seed-specific lignification process.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2020 ◽  
Author(s):  
lin fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Germplasm Conservation ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis

Abstract Backgrounds: Paphiopedilum is an important genus of the orchid family Orchidaceae and has high horticultural value. The wild populations are under threat of extinction because of overcollection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts their germplasm conservation and commercial production. The factors inhibiting germination are largely unknown.Results: In this study, large amounts of non-methylated lignin accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. The transcriptome profiles of P. armeniacum seed at different development stages were compared to explore the molecular clues for non-methylated lignin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism during seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathway displayed different expression patterns during the lignification process. PAL, 4CL, HCT, and CSE upregulation was associated with C and H lignin accumulation. The expression of CCoAOMT, F5H, and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes in seeds and vegetative tissues. Conclusions: This work demonstrated the plasticity of natural lignin polymer assembly in seed and provided a better understanding of the molecular mechanism of seed-specific lignification process.

scholarly journals Transcriptome and Metabolome Analysis Revealed the Freezing Resistance Mechanism in 60-Year-Old Overwintering Camellia sinensis

Biology ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 996
Author(s):  
Hui Wu ◽  
Zixian Wu ◽  
Yuanheng Wang ◽  
Jie Ding ◽  
Yalin Zheng ◽  
...  
Keyword(s):  
Stomatal Closure ◽  
Resistance Mechanism ◽  
Enrichment Analysis ◽  
Resistance Breeding ◽  
Acid Synthesis ◽  
Freezing Stress ◽  
Metabolome Analysis ◽  
Freezing Resistance ◽  
Phenylpropanoid Biosynthesis ◽  
Significant Enrichment

Freezing stress in winter is the biggest obstacle to the survival of C. sinensis in mid-latitude and high-latitude areas, which has a great impact on the yield, quality, and even life of C. sinensis every year. In this study, transcriptome and metabolome were used to clarify the freezing resistance mechanism of 60-year-old natural overwintering C. sinensis under freezing stress. Next, 3880 DEGs and 353 DAMs were obtained. The enrichment analysis showed that pathways of MAPK and ABA played a key role in the signal transduction of freezing stress, and Pyr/PYL-PP2C-SnRK2 in the ABA pathway promoted stomatal closure. Then, the water holding capacity and the freezing resistance of C. sinensis were improved. The pathway analysis showed that DEGs and DAMs were significantly enriched and up-regulated in the three-related pathways of phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and flavonoid biosynthesis. In addition, the carbohydrate and fatty acid synthesis pathways also had a significant enrichment, and the synthesis of these substances facilitated the freezing resistance. These results are of great significance to elucidate the freezing resistance mechanism and the freezing resistance breeding of C. sinensis.

scholarly journals NoRCE: non-coding RNA sets cis enrichment tool

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gulden Olgun ◽  
Afshan Nabi ◽  
Oznur Tastan
Keyword(s):  
Expression Patterns ◽  
Target Prediction ◽  
Enrichment Analysis ◽  
Fruit Fly ◽  
Relevant Information ◽  
R Package ◽  
Data Repository ◽  
Biologically Relevant ◽  
Gene Sets ◽  
Data Files

Abstract Background While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. Results We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. Conclusions NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users’ preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE.

scholarly journals Transcriptome analysis and molecular mechanism of linseed (Linum usitatissimum L.) drought tolerance under repeated drought using single-molecule long-read sequencing

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Wang ◽  
Lei Wang ◽  
Ling Wang ◽  
Meilian Tan ◽  
Collins O. Ogutu ◽  
...  
Keyword(s):  
Dna Repair ◽  
Drought Tolerance ◽  
Single Molecule ◽  
Linum Usitatissimum ◽  
Expression Patterns ◽  
Transcriptional Response ◽  
Enrichment Analysis ◽  
Resistant Variety ◽  
Proline Biosynthesis ◽  
Interacting Protein

Abstract Background Oil flax (linseed, Linum usitatissimum L.) is one of the most important oil crops., However, the increases in drought resulting from climate change have dramatically reduces linseed yield and quality, but very little is known about how linseed coordinates the expression of drought resistance gene in response to different level of drought stress (DS) on the genome-wide level. Results To explore the linseed transcriptional response of DS and repeated drought (RD) stress, we determined the drought tolerance of different linseed varieties. Then we performed full-length transcriptome sequencing of drought-resistant variety (Z141) and drought-sensitive variety (NY-17) under DS and RD stress at the seedling stage using single-molecule real-time sequencing and RNA-sequencing. Gene Ontology (GO) and reduce and visualize GO (REVIGO) enrichment analysis showed that upregulated genes of Z141 were enriched in more functional pathways related to plant drought tolerance than those of NY-17 were under DS. In addition, 4436 linseed transcription factors were identified, and 1190 were responsive to stress treatments. Moreover, protein-protein interaction (PPI) network analysis showed that the proline biosynthesis pathway interacts with stress response genes through RAD50 (DNA repair protein 50) interacting protein 1 (RIN-1). Finally, proline biosynthesis and DNA repair structural gene expression patterns were verified by RT- PCR. Conclusions The drought tolerance of Z141 may be related to its upregulation of drought tolerance genes under DS. Proline may play an important role in linseed drought tolerance by maintaining cell osmotic and protecting DNA from ROS damage. In summary, this study provides a new perspective to understand the drought adaptability of linseed.

scholarly journals Plasma Metabolome Profiling Identifies Metabolic Subtypes of Pancreatic Ductal Adenocarcinoma

Cells ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1821
Author(s):  
Ujjwal Mukund Mahajan ◽  
Ahmed Alnatsha ◽  
Qi Li ◽  
Bettina Oehrle ◽  
Frank-Ulrich Weiss ◽  
...  
Keyword(s):  
Pancreatic Ductal Adenocarcinoma ◽  
Enrichment Analysis ◽  
Response Prediction ◽  
Ductal Adenocarcinoma ◽  
Pathway Enrichment Analysis ◽  
Metabolome Analysis ◽  
Dismal Prognosis ◽  
Chemotherapeutic Response ◽  
Plasma Metabolome ◽  
Metabolome Profiling

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers. Developing biomarkers for early detection and chemotherapeutic response prediction is crucial to improve the dismal prognosis of PDAC patients. However, molecular cancer signatures based on transcriptome analysis do not reflect intratumoral heterogeneity. To explore a more accurate stratification of PDAC phenotypes in an easily accessible matrix, plasma metabolome analysis using MxP® Global Profiling and MxP® Lipidomics was performed in 361 PDAC patients. We identified three metabolic PDAC subtypes associated with distinct complex lipid patterns. Subtype 1 was associated with reduced ceramide levels and a strong enrichment of triacylglycerols. Subtype 2 demonstrated increased abundance of ceramides, sphingomyelin and other complex sphingolipids, whereas subtype 3 showed decreased levels of sphingolipid metabolites in plasma. Pathway enrichment analysis revealed that sphingolipid-related pathways differ most among subtypes. Weighted correlation network analysis (WGCNA) implied PDAC subtypes differed in their metabolic programs. Interestingly, a reduced expression among related pathway genes in tumor tissue was associated with the lowest survival rate. However, our metabolic PDAC subtypes did not show any correlation to the described molecular PDAC subtypes. Our findings pave the way for further studies investigating sphingolipids metabolisms in PDAC.

scholarly journals Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 82
Author(s):  
Yunxiao Wei ◽  
Guoliang Li ◽  
Shujiang Zhang ◽  
Shifan Zhang ◽  
Hui Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Female Parent ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Transcriptional Changes ◽  
Aa Genome ◽  
High Degree

Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.

scholarly journals Effects of corn steep liquor on β-poly(l-malic acid) production in Aureobasidium melanogenum

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Genan Wang ◽  
Bingyi Shi ◽  
Pan Zhang ◽  
Tingbin Zhao ◽  
Haisong Yin ◽  
...  
Keyword(s):  
Malic Acid ◽  
Low Cost ◽  
Corn Steep Liquor ◽  
Enrichment Analysis ◽  
Tca Cycle ◽  
Water Soluble ◽  
Growth And Yield ◽  
The Tca Cycle ◽  
Steep Liquor ◽  
Aureobasidium Melanogenum

Abstractβ-poly(l-malic acid) (PMLA) is a water-soluble biopolymer used in medicine, food, and other industries. However, the low level of PMLA biosynthesis in microorganisms limits its further application in the biotechnological industry. In this study, corn steep liquor (CSL), which processes high nutritional value and low-cost characteristics, was selected as a growth factor to increase the PMLA production in strain, Aureobasidium melanogenum, and its metabolomics change under the CSL addition was investigated. The results indicated that, with 3 g/L CSL, PMLA production, cell growth, and yield (Yp/x) were increased by 32.76%, 41.82%, and 47.43%, respectively. The intracellular metabolites of A. melanogenum, such as amino acids, organic acids, and key intermediates in the TCA cycle, increased after the addition of CSL, and the enrichment analysis showed that tyrosine may play a major role in the PMLA biosynthesis. The results presented in this study demonstrated that the addition of CSL would be an efficient approach to improve PMLA production.

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