scholarly journals Transcriptome analysis reveals candidate genes involved in luciferin metabolism inLuciola aquatilis(Coleoptera: Lampyridae)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2534 ◽  
Author(s):  
Wanwipa Vongsangnak ◽  
Pramote Chumnanpuen ◽  
Ajaraporn Sriboonlert
Keyword(s):  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Biosynthetic Pathway ◽  
De Novo ◽  
Rt Pcr ◽  
Reverse Transcription Pcr ◽  
Key Enzyme ◽  
Coleopteran Insect ◽  
Living Organisms ◽  
Pathway Databases

Bioluminescence, which living organisms such as fireflies emit light, has been studied extensively for over half a century. This intriguing reaction, having its origins in nature where glowing insects can signal things such as attraction or defense, is now widely used in biotechnology with applications of bioluminescence and chemiluminescence. Luciferase, a key enzyme in this reaction, has been well characterized; however, the enzymes involved in the biosynthetic pathway of its substrate, luciferin, remains unsolved at present. To elucidate the luciferin metabolism, we performed ade novotranscriptome analysis using larvae of the firefly species,Luciola aquatilis. Here, a comparative analysis is performed with the model coleopteran insectTribolium casteneumto elucidate the metabolic pathways inL. aquatilis. Based on a template luciferin biosynthetic pathway, combined with a range of protein and pathway databases, and various prediction tools for functional annotation, the candidate genes, enzymes, and biochemical reactions involved in luciferin metabolism are proposed forL. aquatilis. The candidate gene expression is validated in the adultL. aquatilisusing reverse transcription PCR (RT-PCR). This study provides useful information on the bio-production of luciferin in the firefly and will benefit to future applications of the valuable firefly bioluminescence system.

scholarly journals De novo transcriptome analysis of Lantana camara L. revealed candidate genes involved in phenylpropanoid biosynthesis pathway

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Muzammil Shah ◽  
Hesham F. Alharby ◽  
Khalid Rehman Hakeem ◽  
Niaz Ali ◽  
Inayat Ur Rahman ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Transcriptome Analysis ◽  
De Novo ◽  
Lantana Camara ◽  
Biosynthesis Pathway ◽  
De Novo Transcriptome ◽  
Phenylpropanoid Biosynthesis

scholarly journals Salt-responsive transcriptome analysis of triticale reveals candidate genes involved in the key metabolic pathway in response to salt stress

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Chaohong Deng ◽  
Zhibin Zhang ◽  
Guorong Yan ◽  
Fan Wang ◽  
Lianjia Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Regulatory Mechanism ◽  
De Novo ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Time Points

AbstractTriticale is tolerant of many environmental stresses, especially highly resistant to salt stress. However, the molecular regulatory mechanism of triticale seedlings under salt stress conditions is still unclear so far. In this study, a salt-responsive transcriptome analysis was conducted to identify candidate genes or transcription factors related to salt tolerance in triticale. The root of salt-tolerant triticale cultivars TW004 with salt-treated and non-salt stress at different time points were sampled and subjected to de novo transcriptome sequencing. Total 877,858 uniquely assembled transcripts were identified and most contigs were annotated in public databases including nr, GO, KEGG, eggNOG, Swiss-Prot and Pfam. 59,280, 49,345, and 85,922 differentially expressed uniquely assembled transcripts between salt treated and control triticale root samples at three different time points (C12_vs_T12, C24_vs_T24, and C48_vs_T48) were identified, respectively. Expression profile and functional enrichment analysis of DEGs found that some DEGs were significantly enriched in metabolic pathways related to salt tolerance, such as reduction–oxidation pathways, starch and sucrose metabolism. In addition, several transcription factor families that may be associated with salt tolerance were also identified, including AP2/ERF, NAC, bHLH, WRKY and MYB. Furthermore, 14 DEGs were selected to validate the transcriptome profiles via quantitative RT-PCR. In conclusion, these results provide a foundation for further researches on the regulatory mechanism of triticale seedlings adaptation to salt stress in the future.

De novo transcriptome analysis and identification of candidate genes associated with triterpenoid biosynthesis in Trichosanthes cucumerina L.

2021 ◽  
Author(s):  
Pornpatsorn Lertphadungkit ◽  
Xue Qiao ◽  
Supaart Sirikantaramas ◽  
Veena Satitpatipan ◽  
Min Ye ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Transcriptome Analysis ◽  
De Novo ◽  
De Novo Transcriptome

scholarly journals Elucidating biosynthetic pathway of piperine using comparative transcriptome analysis of leaves, root and spike in Piper longum L

2021 ◽  
Author(s):  
Prem Kumar Dantu ◽  
Mrinalini Prasad ◽  
Rajiv Ranjan
Keyword(s):  
Transcriptome Analysis ◽  
Biosynthetic Pathway ◽  
De Novo ◽  
Gene Families ◽  
Comparative Transcriptome ◽  
Illumina Platform ◽  
Piper Longum ◽  
Comparative Transcriptome Analysis ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractPiper longum (Pipli; Piperaceae) is an important spice valued for its pungent alkaloids, especially piperine. Albeit, its importance, the mechanism of piperine biosynthesis is still poorly understood. The Next Generation Sequencing (NGS) for P. longum leaves, root and spikes was performed using Illumina platform, which generated 16901456, 54993496 and 22900035, respectively of high quality reads. In de novo assembly P. longum 173381 numbers of transcripts were analyzed. Analysis of transcriptome data from leaf, root and spike showed gene families that were involved in the biosynthetic pathway of piperine and other secondary metabolites. To validate differential expression of the identified genes, 27 genes were randomly selected to confirm the expression level by quantitative real time PCR (qRT-PCR) based on the up regulation and down regulation of differentially expressed genes obtained through comparative transcriptome analysis of leaves and spike of P. longum. With the help of UniProt database the function of all characterized genes was generated.

scholarly journals Mining of candidate genes involved in the biosynthesis of dextrorotatory borneol in Cinnamomum burmannii by transcriptomic analysis on three chemotypes

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9311 ◽  
Author(s):  
Zerui Yang ◽  
Wenli An ◽  
Shanshan Liu ◽  
Yuying Huang ◽  
Chunzhu Xie ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Biosynthetic Pathway ◽  
De Novo ◽  
Expression Patterns ◽  
Biological Synthesis ◽  
Terpenoid Biosynthesis ◽  
Monoterpene Synthase ◽  
Patent Remedies ◽  
Long Time ◽  
Additional Approach

Background Dextrorotatory borneol (D-borneol), a cyclic monoterpene, is widely used in traditional Chinese medicine as an efficient topical analgesic drug. Fresh leaves of Cinnamomum trees, e.g., C. burmannii and C. camphor, are the main sources from which D-borneol is extracted by steam distillation, yet with low yields. Insufficient supply of D-borneol has hampered its clinical use and production of patent remedies for a long time. Biological synthesis of D-borneol offers an additional approach; however, mechanisms of D-borneol biosynthesis remain mostly unresolved. Hence, it is important and necessary to elucidate the biosynthetic pathway of D-borneol. Results Comparative analysis on the gene expression patterns of different D-borneol production C. burmannii samples facilitates elucidation on the underlying biosynthetic pathway of D-borneol. Herein, we collected three different chemotypes of C. burmannii, which harbor different contents of D-borneol.A total of 100,218 unigenes with an N50 of 1,128 bp were assembled de novo using Trinity from a total of 21.21 Gb clean bases. We used BLASTx analysis against several public databases to annotate 45,485 unigenes (45.38%) to at least one database, among which 82 unigenes were assigned to terpenoid biosynthesis pathways by KEGG annotation. In addition, we defined 8,860 unigenes as differentially expressed genes (DEGs), among which 13 DEGs were associated with terpenoid biosynthesis pathways. One 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and two monoterpene synthase, designated as CbDXS9, CbTPS2 and CbTPS3, were up-regulated in the high-borneol group compared to the low-borneol and borneol-free groups, and might be vital to biosynthesis of D-borneol in C. burmannii. In addition, we identified one WRKY, two BHLH, one AP2/ERF and three MYB candidate genes, which exhibited the same expression patterns as CbTPS2 and CbTPS3, suggesting that these transcription factors might potentially regulate D-borneol biosynthesis. Finally, quantitative real-time PCR was conducted to detect the actual expression level of those candidate genes related to the D-borneol biosynthesis pathway, and the result showed that the expression patterns of the candidate genes related to D-borneol biosynthesis were basically consistent with those revealed by transcriptome analysis. Conclusions We used transcriptome sequencing to analyze three different chemotypes of C. burmannii, identifying three candidate structural genes (one DXS, two monoterpene synthases) and seven potential transcription factor candidates (one WRKY, two BHLH, one AP2/ERF and three MYB) involved in D-borneol biosynthesis. These results provide new insight into our understanding of the production and accumulation of D-borneol in C. burmannii.

scholarly journals De novo leaf and root transcriptome analysis to explore biosynthetic pathway of Celangulin V in Celastrus angulatus maxim

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Weiguo Li ◽  
Ranran Xu ◽  
Xiaoguang Yan ◽  
Dongmei Liang ◽  
Lei Zhang ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Biosynthetic Pathway ◽  
De Novo ◽  
Root Transcriptome
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