scholarly journals Transcriptomic Revelation of Phenolic Compounds Involved in Aluminum Toxicity Responses in Roots of Cunninghamia lanceolata (Lamb.) Hook

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 835 ◽  
Author(s):  
Ma ◽  
Lin
Keyword(s):  
South China ◽  
Molecular Mechanisms ◽  
Average Length ◽  
Al Toxicity ◽  
Chinese Fir ◽  
Cunninghamia Lanceolata ◽  
Differentially Expressed ◽  
Primary Metabolism ◽  
Al Stress ◽  
Root Responses

: Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is one of the most important coniferous evergreen tree species in South China due to its desirable attributes of fast growth and production of strong and hardy wood. However, the yield of Chinese fir is often inhibited by aluminum (Al) toxicity in acidic soils of South China. Understanding the molecular mechanisms of Chinese fir root responses to Al toxicity might help to further increase its productivity. Here we used the Illumina Hiseq4000 platform to carry out transcriptome analysis of Chinese fir roots subjected to Al toxicity conditions. A total of 88.88 Gb of clean data was generated from 12 samples and assembled into 105,732 distinct unigenes. The average length and N50 length of these unigenes were 839 bp and 1411 bp, respectively. Among them, 58362 unigenes were annotated through searches of five public databases (Nr: NCBI non-redundant protein sequences, Swiss-Prot: A manually annotated and reviewed protein sequence database, GO: Gene Ontology, KOG/COG: Clusters of Orthologous Groups of proteins, and KEGG: the Kyoto Encyclopedia of Genes and Genomes database), which led to association of unigenes with 44 GO terms. Plus, 1615 transcription factors (TFs) were functionally classified. Then, differentially expressed genes (DEGs, |log2(fold change)| ≥ 1 and FDR ≤ 0.05) were identified in comparisons labelled TC1 (CK-72 h/CK-1 h) and TC2 (Al-72 h/Al-1 h). A large number of TC2 DEGs group were identified, with most being down-regulated under Al stress, while TC1 DEGs were primarily up-regulated. Combining GO, KEGG, and MapMan pathway analysis indicated that many DEGs are involved in primary metabolism, including cell wall metabolism and lipid metabolism, while other DEGs are associated with signaling pathways and secondary metabolism, including flavonoids and phenylpropanoids metabolism. Furthermore, TFs identified in TC1 and TC2 DEGs represented 21 and 40 transcription factor families, respectively. Among them, expression of bHLH, C2H2, ERF, bZIP, GRAS, and MYB TFs changed considerably under Al stress, which suggests that these TFs might play crucial roles in Chinese fir root responses to Al toxicity. These differentially expressed TFs might act in concert with flavonoid and phenylpropanoid pathway genes in fulfilling of key roles in Chinese fir roots responding to Al toxicity.

Identification and analysis of differentially expressed genes in differentiating xylem of Chinese fir (Cunninghamia lanceolata) by suppression subtractive hybridization

Genome ◽  
2007 ◽  
Vol 50 (12) ◽  
pp. 1141-1155 ◽  
Author(s):  
Guifeng Wang ◽  
Yan Gao ◽  
Liwei Yang ◽  
Jisen Shi
Keyword(s):  
Real Time ◽  
Suppression Subtractive Hybridization ◽  
Real Time Pcr ◽  
Molecular Mechanisms ◽  
Subtractive Hybridization ◽  
Wood Formation ◽  
Chinese Fir ◽  
Cunninghamia Lanceolata ◽  
Differentially Expressed ◽  
Xylem Differentiation

Wood is an important raw material for global industries with rapidly increasing demand. To isolate the genes differentially expressed during xylogenesis of Chinese fir ( Cunninghamia lanceolata (Lamb.) Hook.), we used a novel system. Forward and reverse subtracted cDNA libraries were constructed using the suppression subtractive hybridization method; for the forward library we used cDNA from the mutant Dugansha as the tester and cDNA from the wild-type clone Jurong 0 as the driver, and for the reverse library we used Jurong 0 cDNA as the tester and Dugansha cDNA as the driver. Transcriptional profiling was performed using a macroarray with 4 digoxigenin-labeled probes. We obtained 618 and 409 clones from the forward and the reverse subtracted library, respectively. A total of 405 unique expressed sequence tags (ESTs) were obtained. Forty percent of the ESTs exhibited homologies with proteins of known function and fell into 4 major classes: metabolism, cell wall biogenesis and remodeling, signal transduction, and stress. Real-time PCR was performed to confirm the results. The expression levels of 11 selected ESTs were consistent with both macroarray and real-time PCR results. The systematic analysis of genes involved in wood formation in Chinese fir provides valuable insights into the molecular mechanisms involved in xylem differentiation and is an important resource for forest research that can be directed toward understanding the genetic control of wood formation and future endeavors to modify wood and fiber properties for industrial use.

scholarly journals Transcriptome and Gene Expression Analysis of Cylas formicarius (Coleoptera: Brentidae) During Different Development Stages

2016 ◽  
Vol 16 (1) ◽  
Author(s):  
Juan Ma ◽  
Rongyan Wang ◽  
Xiuhua Li ◽  
Bo Gao ◽  
Shulong Chen
Keyword(s):  
Sweet Potato ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Average Length ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Cylas Formicarius ◽  
Important Pest

Abstract The sweet potato weevil, Cylas formicarius (F.) (Coleoptera: Brentidae), is an important pest of sweet potato worldwide. However, there is limited knowledge on the molecular mechanisms underlying growth and differentiation of C. formicarius. The transcriptomes of the eggs, second instar larvae, third instar larvae (L3), pupae, females, and males of C. formicarius were sequenced using Illumina sequencing technology for obtaining global insights into developing transcriptome characteristics and elucidating the relative functional genes. A total of 54,255,544 high-quality reads were produced, trimmed, and de novo assembled into 115,281 contigs. 61,686 unigenes were obtained, with an average length of 1,009 nt. Among these unigenes, 17,348 were annotated into 59 Gene Ontology (GO) terms and 12,660 were assigned to 25 Cluster of Orthologous Groups classes, whereas 24,796 unigenes were mapped to 258 pathways. Differentially expressed unigenes between various developmental stages of C. formicarius were detected. Higher numbers of differentially expressed genes (DEGs) were recorded in the eggs versus L3 and eggs versus male samples (2,141 and 2,058 unigenes, respectively) than the others. Genes preferentially expressed in each stage were also identified. GO and pathway-based enrichment analysis were used to further investigate the functions of the DEGs. In addition, the expression profiles of ten DEGs were validated by quantitative real-time PCR. The transcriptome profiles presented in this study and these DEGs detected by comparative analysis of different developed stages of C. formicarius will facilitate the understanding of the molecular mechanism of various living process and will contribute to further genome-wide research.

Physiological and transcriptional responses of broad bean (Vicia faba L.) leaves to aluminium stress

2013 ◽  
Vol 152 (6) ◽  
pp. 894-905
Author(s):  
H. N. XU ◽  
K. WANG ◽  
Y. N. ZHANG ◽  
Q. CHEN ◽  
L. M. CHEN ◽  
...  
Keyword(s):  
Cell Death ◽  
Molecular Mechanisms ◽  
Broad Bean ◽  
Stomatal Closure ◽  
Al Toxicity ◽  
Protein Carbonyls ◽  
Chloroplast Structure ◽  
Transcriptional Responses ◽  
Al Stress ◽  
Al Treatment

SummaryAluminium (Al) toxicity is the major factor-limiting crop productivity in acid soils. In the present study, physiological and transcriptional responses of broad bean leaves to Al stress were investigated. Malondialdehyde (MDA) content, H2O2 content and protein carbonyls (PC) level in leaves were increased after 100 μm AlCl3 stress treatment, whereas the total protein content was decreased, compared with the plants without Al treatment. Stomatal closure in leaves of broad bean was increased after Al stress, suggesting that the photosynthesis rate might be affected by Al stress. The relative citrate secretion in leaves was decreased after Al treatment for 24 h according to the 13C-NMR analysis, indicating that citrate in leaves might be transported to the root to chelate Al3+. To investigate the molecular mechanisms of Al toxicity in leaves of broad bean, a suppression subtractive hybridization (SSH) library was constructed to identify up-regulated genes: cDNA from leaves subjected to 12, 24, 48 and 72 h of 50 and 100 μm AlCl3 stress were used as testers and cDNA from leaves subjected to 0 μm AlCl3 treatment for the same lengths of time as above were used as a driver. The SSH analysis identified 156 non-redundant putative Al stress-responsive expressed sequence tags (ESTs) out of 960 clones. The ESTs were categorized into ten functional groups, which were involved in metabolism (0·21), protein synthesis and protein fate (0·10), photosynthesis and chloroplast structure (0·09), transporter (0·08), cell wall related (0·06), signal transduction (0·05), defence, stress and cell death (0·05), energy (0·03), transcription factor (0·03) and unknown proteins (0·30). The effect of Al treatment on expression of 15 selected genes was investigated by reverse transcription polymerase chain reaction (RT–PCR), confirming induction by Al stress. The results indicated that genes involved in organic acid metabolism, transport, photosynthesis and chloroplast structure, defence, stress and cell death might play important roles under Al stress.

Comparative iTRAQ Proteomic Analysis Provides the Molecular Basis of the Metabolites in Cultivated Glycyrrhiza uralensis and its Wild-Type

2020 ◽  
Vol 17 (5) ◽  
pp. 365-378
Author(s):  
Chengcheng Wang ◽  
Lihong Chen ◽  
Zhichen Cai ◽  
Sijing Feng ◽  
Moyi Yue ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Molecular Mechanisms ◽  
Glycyrrhiza Uralensis ◽  
Differentially Expressed ◽  
Primary Metabolism ◽  
Differentially Expressed Proteins ◽  
Metabolite Formation ◽  
Glycyrrhiza Uralensis Fisch ◽  
Significant Difference ◽  
Metabolite Synthesis

Background: Licorice is an herbal medicine applied extensively worldwide, and most of the licorice for clinical consumption is provided by Glycyrrhiza uralensis Fisch. Evidence suggests that there is a significant difference in the metabolite composition of licorice from different ecotypes. Objective: To better understand the proteomic changes and molecular mechanisms of metabolite formation in wild and cultivated Glycyrrhiza uralensis Fisch. Methods: Firstly, we established a proteome database by annotating protein sequences according to the genomic and transcriptomic data of G. uralensis. Then, iTRAQ and LC-MS/MS were applied to detect significant protein changes between cultivated and wild G. uralensis. A total of 2751 validated proteins were obtained with high confidence, and 333 were differentially expressed. Differentially expressed proteins were identified and analysed by GO, KEGG, and STRING for network and pathway enrichment. Ultimately, we combined the iTRAQ results with our previous investigation on metabolites to understand the molecular mechanisms underlying metabolite accumulation. Results: The results showed that differentially expressed proteins were mainly involved in the anabolism of carbohydrates and important amino acids that participate in primary metabolism and secondary metabolite synthesis. Another important pathway is the synthesis of flavonoids, which are generally accepted as important bioactive constituents of G. uralensis, and the accumulation of flavonoids in different synthesis stages in two ecotypes of G. uralensis was diverse. Therefore, the differentially abundant proteins in wild and cultivated G. uralensis possibly resulted in differences in medicinal compounds. Conclusion: Our study will provide novel clues for revealing the molecular mechanism of secondary metabolite synthesis as well as quality formation in wild and cultivated G. uralensis.

scholarly journals Transcriptomic Analysis Identifies New Non-Target Site Glyphosate-Resistance Genes in Conyza bonariensis

Plants ◽  
2019 ◽  
Vol 8 (6) ◽  
pp. 157 ◽  
Author(s):  
Cristiano Piasecki ◽  
Yongil Yang ◽  
Daiane P. Benemann ◽  
Frederico S. Kremer ◽  
Vanessa Galli ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Target Genes ◽  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Glyphosate Resistance ◽  
Target Site ◽  
Differentially Expressed ◽  
Irreversible Damage ◽  
Conyza Bonariensis

Conyza bonariensis (hairy fleabane) is one of the most problematic and widespread glyphosate-resistant weeds in the world. This highly competitive weed species significantly interferes with crop growth and substantially decreases crop yield. Despite its agricultural importance, the molecular mechanisms of glyphosate resistance are still unknown. The present RNA-Seq study was performed with the goal of identifying differentially expressed candidate transcripts (genes) related to metabolism-based non-target site glyphosate resistance in C. bonariensis. The whole-transcriptome was de novo assembled from glyphosate-resistant and -sensitive biotypes of C. bonariensis from Southern Brazil. The RNA was extracted from untreated and glyphosate-treated plants at several timepoints up to 288 h after treatment in both biotypes. The transcriptome assembly produced 90,124 contigs with an average length of 777 bp and N50 of 1118 bp. In response to glyphosate treatment, differential gene expression analysis was performed on glyphosate-resistant and -sensitive biotypes. A total of 9622 genes were differentially expressed as a response to glyphosate treatment in both biotypes, 4297 (44.6%) being up- and 5325 (55.4%) down-regulated. The resistant biotype presented 1770 up- and 2333 down-regulated genes while the sensitive biotype had 2335 and 2800 up- and down-regulated genes, respectively. Among them, 974 up- and 1290 down-regulated genes were co-expressed in both biotypes. In the present work, we identified 41 new candidate target genes from five families related to herbicide transport and metabolism: 19 ABC transporters, 10 CYP450s, one glutathione S-transferase (GST), five glycosyltransferases (GT), and six genes related to antioxidant enzyme catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD). The candidate genes may participate in metabolic-based glyphosate resistance via oxidation, conjugation, transport, and degradation, plus antioxidation. One or more of these genes might ‘rescue’ resistant plants from irreversible damage after glyphosate treatment. The 41 target genes we report in the present study may inform further functional genomics studies, including gene editing approaches to elucidate glyphosate-resistance mechanisms in C. bonariensis.

Litterfall production and nutrient return in different-aged Chinese fir (Cunninghamia lanceolata) plantations in South China

2015 ◽  
Vol 26 (1) ◽  
pp. 79-89 ◽  
Author(s):  
Lili Zhou ◽  
Addo-Danso Daniel Shalom ◽  
Pengfei Wu ◽  
Shubin Li ◽  
Yayun Jia ◽  
...  
Keyword(s):  
South China ◽  
Chinese Fir ◽  
Cunninghamia Lanceolata ◽  
Nutrient Return ◽  
Litterfall Production

scholarly journals Analysis of Differentially Expressed Genes of Chrysoperla sinica Related to Flight Capacity by Transcriptome

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhong-Fang Liu ◽  
Yao-yao Liang ◽  
Xiao-ting Sun ◽  
Jing Yang ◽  
Peng-Jiu Zhang ◽  
...  
Keyword(s):  
Biological Control ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Insect Pests ◽  
Average Length ◽  
Differentially Expressed ◽  
Acid Decarboxylase ◽  
Flight Capacity ◽  
Different Ages

Abstract The lacewing Chrysoperla sinica (Tjeder) is a common natural enemy of many insect pests in China and is frequently employed for biological control programs. Adults make migratory flights after emergence, which reduces their effectiveness as biological control agents. Previously, we proved that 2-d-old unmated females exhibited significantly stronger flight ability than 3-d-old ones. Meanwhile, 3-d-old unmated adults flew significantly longer distances than mated ones. In this study, Illumina RNA sequencing was performed to characterize differentially expressed genes (DEGs) between virgin and mated adults of different ages in a single female strain of C. sinica. In total, 713,563,726 clean reads were obtained and de novo assembled into 109,165 unigenes with an average length of 847 bp (N50 of 1,754 bp), among which 4,382 (4.01%) unigenes matched known proteins. Based on these annotations, many putative transcripts were related to C. sinica’s flight capacity and muscle structure, energy supply, growth, development, environmental adaptability, and metabolism of nutritional components and bioactive components. In addition, the differential expression of transcripts between different ages and mating status were analyzed, and DEGs participating in flight capacity and muscles were detected, including glutathione hydrolase, NAD-specific glutamate dehydrogenase, aminopeptidase, and acidic amino acid decarboxylase. The DEGs with functions associated with flight capacity and muscles exhibited higher transcript levels for younger (2 d--old) virgins. This comprehensive C. sinica transcriptomic data provide a foundation for a better understanding of the molecular mechanisms underlying the flight capacity to meet the physiological demands of flight muscles in C. sinica.

scholarly journals Shared differentially expressed genes of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) seedlings under low nitrogen and phosphorus stress

2017 ◽  
Author(s):  
JianHui Li ◽  
GuiFang Ma ◽  
DingWei Luo ◽  
ZaiKang Tong ◽  
Jinliang Xu ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Chinese Fir ◽  
Cunninghamia Lanceolata ◽  
Utilization Efficiency ◽  
Differentially Expressed ◽  
Nitrogen And Phosphorus ◽  
Stress Group ◽  
Phosphorus Stress ◽  
Low Nitrogen

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is an excellent fast-growing timber species and has significant value in the forestry industry. In order to increase the nitrogen and phosphorus absorption and utilization in Chinese fir, shared differentially expressed genes under low nitrogen and phosphorus stress were screened in this study. Seedling of Chinese fir clone X6 was cultivated in aeroponic system with 3 treatments, namely, low nitrogen (LN), low phosphorus (LP) and a control check (with nitrogen and phosphorus sufficient, CK). After 4 months of treatment, the roots from the LN, LP and CK groups were collected and transcriptome sequencing was done by LC Sciences (USA) using an Illumina platform. When comparing the LN stress group with the CK group, 977 SDGEs were detected, 264 of which had KEGG annotations; 931 SDGEs were detected when comparing the LP stress group with the CK group, of which 189 had KEGG annotations; 297 SDGEs were detected in both the LN stress and LP stress groups, 78 of which had KEGG annotations representing 98 metabolic pathways. Among the 78 selected SDEGs that were differentially expressed under both LN and LP stress conditions, Twenty-one SDEGs were selected based on the metabolic pathways that nitrogen and phosphorus are involved in, these genes are PNR, PSBA, EGLC, GLC, END, BGLU, AMY, A1E, PAL, GOGAT, NIR1, NIR2, C4M, PAL, PRDX6, POX, CCR, CCoAOMT, FDH, CHS and ANR. These genes can potentially be used in breeding to improve both nitrogen and phosphorus utilization efficiency in Chinese fir.

scholarly journals Shared differentially expressed genes of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) seedlings under low nitrogen and phosphorus stress

2017 ◽  
Author(s):  
JianHui Li ◽  
GuiFang Ma ◽  
DingWei Luo ◽  
ZaiKang Tong ◽  
Jinliang Xu ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Chinese Fir ◽  
Cunninghamia Lanceolata ◽  
Utilization Efficiency ◽  
Differentially Expressed ◽  
Nitrogen And Phosphorus ◽  
Stress Group ◽  
Phosphorus Stress ◽  
Low Nitrogen

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is an excellent fast-growing timber species and has significant value in the forestry industry. In order to increase the nitrogen and phosphorus absorption and utilization in Chinese fir, shared differentially expressed genes under low nitrogen and phosphorus stress were screened in this study. Seedling of Chinese fir clone X6 was cultivated in aeroponic system with 3 treatments, namely, low nitrogen (LN), low phosphorus (LP) and a control check (with nitrogen and phosphorus sufficient, CK). After 4 months of treatment, the roots from the LN, LP and CK groups were collected and transcriptome sequencing was done by LC Sciences (USA) using an Illumina platform. When comparing the LN stress group with the CK group, 977 SDGEs were detected, 264 of which had KEGG annotations; 931 SDGEs were detected when comparing the LP stress group with the CK group, of which 189 had KEGG annotations; 297 SDGEs were detected in both the LN stress and LP stress groups, 78 of which had KEGG annotations representing 98 metabolic pathways. Among the 78 selected SDEGs that were differentially expressed under both LN and LP stress conditions, Twenty-one SDEGs were selected based on the metabolic pathways that nitrogen and phosphorus are involved in, these genes are PNR, PSBA, EGLC, GLC, END, BGLU, AMY, A1E, PAL, GOGAT, NIR1, NIR2, C4M, PAL, PRDX6, POX, CCR, CCoAOMT, FDH, CHS and ANR. These genes can potentially be used in breeding to improve both nitrogen and phosphorus utilization efficiency in Chinese fir.

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