scholarly journals Transcriptome analysis of Aconitum carmichaelii and exploration of the salsolinol biosynthetic pathway

Fitoterapia ◽  
2020 ◽  
Vol 140 ◽  
pp. 104412 ◽  
Author(s):  
Yuxia Yang ◽  
Ping Hu ◽  
Xianjian Zhou ◽  
Ping Wu ◽  
Xinxin Si ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Biosynthetic Pathway ◽  
Aconitum Carmichaelii

scholarly journals Transcriptome Analysis of Aconitum carmichaelii and Exploration of the Salsolinol Biosynthetic Pathway

2019 ◽  
Author(s):  
Yuxia Yang ◽  
Ping Hu ◽  
Xianjian Zhou ◽  
Ping Wu ◽  
Xinxin Si ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Theoretical Basis ◽  
Biosynthetic Pathway ◽  
Target Genes ◽  
Shikimate Pathway ◽  
Biosynthesis Pathway ◽  
Alkaloid Biosynthesis ◽  
Diterpenoid Alkaloids ◽  
Protein Databases ◽  
Aconitum Carmichaelii

Abstract Background Aconitum carmichaelii has been used in traditional Chinese medicine for treating various diseases for several thousand years. The biosynthetic pathway of some alkaloids such as C19-diterpenoid alkaloids has been reported, but pathways in different varieties of A. carmichaelii remain unknown. Herein, we performed transcriptome analysis of varieties A. carmichaelii and characterized the biosynthetic pathway of salsolinol. The results expand our knowledge of alkaloids biosynthesis, and provide a theoretical basis for analysing differences in alkaloids biosynthesis patterns in different varieties. Results A total of 56 million raw reads (8.28 G) and 55 million clean reads (8.24 G) were obtained from two varieties (Z175 and R184) leaf transcriptomes, respectively, and 176,793 unigenes were annotated using six protein databases. This yielded 6,873 differentially expressed genes (DEGs) in the two varieties, of which 281 are involved in the salsolinol biosynthetic pathway, including 158 and 75 related to glycolysis and the shikimate pathway, respectively. Furthermore, 843 DEGs were found to be involved in the formation of C19-diterpenoid alkaloids, with 34 differed between the two varieties. These target genes were analysed to explore differences in C19-diterpenoid alkaloid biosynthesis in Z175 and R184. In addition, 322 DEGs encoding transcription factors potentially related to alkaloid accumulation were identified. Conclusions The biosynthesis pathway for C19-diterpenoid alkaloids and salsolinol included 34 and 24 DEGs in Z175 and R184, respectively. Thus, genes involved in alkaloid biosynthesis and accumulation differ between varieties. The mechanisms underlying the differences and their relevance require further exploration.

scholarly journals Comparative transcriptome analysis of root, stem, and leaf tissues of Entada phaseoloides reveals potential genes involved in triterpenoid saponin biosynthesis

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Weifang Liao ◽  
Zhinan Mei ◽  
Lihong Miao ◽  
Pulin Liu ◽  
Ruijie Gao
Keyword(s):  
Transcriptome Analysis ◽  
Biosynthetic Pathway ◽  
Triterpenoid Saponin ◽  
Uridine Diphosphate ◽  
Comparative Transcriptome ◽  
Triterpenoid Saponins ◽  
Comparative Transcriptome Analysis ◽  
Saponin Biosynthesis ◽  
Leaf Tissues ◽  
Entada Phaseoloides

Abstract Background Entada phaseoloides (L.) Merr. is an important traditional medicinal plant. The stem of Entada phaseoloides is popularly used as traditional medicine because of its significance in dispelling wind and dampness and remarkable anti-inflammatory activities. Triterpenoid saponins are the major bioactive compounds of Entada phaseoloides. However, genomic or transcriptomic technologies have not been used to study the triterpenoid saponin biosynthetic pathway in this plant. Results We performed comparative transcriptome analysis of the root, stem, and leaf tissues of Entada phaseoloides with three independent biological replicates and obtained a total of 53.26 Gb clean data and 116,910 unigenes, with an average N50 length of 1218 bp. Putative functions could be annotated to 42,191 unigenes (36.1%) based on BLASTx searches against the Non-redundant, Uniprot, KEGG, Pfam, GO, KEGG and COG databases. Most of the unigenes related to triterpenoid saponin backbone biosynthesis were specifically upregulated in the stem. A total of 26 cytochrome P450 and 17 uridine diphosphate glycosyltransferase candidate genes related to triterpenoid saponin biosynthesis were identified. The differential expressions of selected genes were further verified by qPT-PCR. Conclusions The dataset reported here will facilitate the research about the functional genomics of triterpenoid saponin biosynthesis and genetic engineering of Entada phaseoloides.

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 Nitrate-responsive suppression of DMSO respiration in a facultative anaerobic haloarchaeon Haloferax volcanii

2021 ◽  
Author(s):  
Isamu Koyanagi ◽  
Hideo Dohra ◽  
Taketomo Fujiwara
Keyword(s):  
Transcriptome Analysis ◽  
Biosynthetic Pathway ◽  
Anaerobic Bacteria ◽  
Haloferax Volcanii ◽  
Anaerobic Growth ◽  
Nitrate Respiration ◽  
Reporter Assay ◽  
Anaerobic Conditions ◽  
Facultative Anaerobic ◽  
Facultative Anaerobic Bacteria

Haloferax volcanii is a facultative anaerobic haloarchaeon that can grow using nitrate or dimethyl sulfoxide (DMSO) as respiratory substrates in an anaerobic condition. Comparative transcriptome analysis of denitrifying and aerobic cells of H. volcanii indicated extensive changes in the gene expression involving activation of denitrification, suppression of DMSO respiration, and conversion of the heme biosynthetic pathway under denitrifying condition. Anaerobic growth of H. volcanii by DMSO respiration was inhibited at nitrate concentrations lower than 1 mM, whereas the nitrate-responsive growth inhibition was not observed in the ΔnarO mutant. A reporter assay experiment demonstrated that transcription of the dms operon was suppressed by nitrate. In contrast, anaerobic growth of the ΔdmsR mutant by denitrification was little affected by addition of DMSO. NarO has been identified as an activator of the denitrification-related genes in response to anaerobic conditions, and here we found that NarO is also involved in nitrate-responsive suppression of the dms operon. Nitrate-responsive suppression of DMSO respiration is known in several bacteria, such as Escherichia coli and photosynthetic Rhodobacter sp. This is the first report to show that a regulatory mechanism that suppresses DMSO respiration in response to nitrate exists not only in bacteria but also in the haloarchaea. IMPORTANCE Haloferax volcanii can grow anaerobically by denitrification (nitrate respiration) or DMSO respiration. In the facultative anaerobic bacteria that can grow by both nitrate respiration and DMSO respiration, nitrate respiration is preferentially induced when both nitrate and DMSO are available as respiratory substrates. The results of transcriptome analysis, growth phenotyping, and reporter assay indicated that DMSO respiration is suppressed in response to nitrate in H. volcanii. The haloarchaea-specific regulator NarO, which activates denitrification under anaerobic conditions, is suggested to be involved in the nitrate-responsive suppression of DMSO respiration.

scholarly journals Comparative transcriptome analysis of root, stem, and leaf tissues of Entada phaseoloides reveals potential genes involved in triterpenoid saponin biosynthesis

2020 ◽  
Author(s):  
Weifang Liao ◽  
Lihong Miao ◽  
Pulin Liu ◽  
Ruijie Gao ◽  
Zhinan Mei
Keyword(s):  
Transcriptome Analysis ◽  
Biosynthetic Pathway ◽  
Triterpenoid Saponin ◽  
Uridine Diphosphate ◽  
Comparative Transcriptome ◽  
Triterpenoid Saponins ◽  
Comparative Transcriptome Analysis ◽  
Saponin Biosynthesis ◽  
Leaf Tissues ◽  
Entada Phaseoloides

Abstract Background Entada phaseoloides (L.) Merr. is an important traditional medicinal plant. The stem of Entada phaseoloides is popularly used as traditional medicine because of its significance in dispelling wind and dampness and remarkable anti-inflammatory activities. Triterpenoid saponins are the major bioactive compounds of Entada phaseoloides. However, genomic or transcriptomic technologies have not been used to study the triterpenoid saponin biosynthetic pathway in this plant.Results We performed comparative transcriptome analysis of the root, stem, and leaf tissues of Entada phaseoloides with three independent biological replicates and obtained a total of 53.26 Gb clean data and 116,910 unigenes, with an average N50 length of 1218 bp. Putative functions could be annotated to 42,191 unigenes (36.1%) based on BLASTx searches against the Non-redundant, Uniprot, KEGG, Pfam, GO, KEGG and COG databases. Most of the unigenes related to triterpenoid saponin backbone biosynthesis were specifically upregulated in the stem. A total of 26 cytochrome P450 and 17 uridine diphosphate glycosyltransferase candidate genes related to triterpenoid saponin biosynthesis were identified. The differential expressions of selected genes were further verified by qPT-PCR.Conclusions The dataset reported here will facilitate the research about the functional genomics of triterpenoid saponin biosynthesis and genetic engineering of Entada phaseoloides .

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

scholarly journals Integrated metabolome and transcriptome analysis of the anthocyanin biosynthetic pathway in relation to color mutation in miniature roses

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jiaojiao Lu ◽  
Qing Zhang ◽  
Lixin Lang ◽  
Chuang Jiang ◽  
Xiaofeng Wang ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Biosynthetic Pathway ◽  
Ornamental Plants ◽  
Syringic Acid ◽  
Flavonoid Pathway ◽  
Color Mutant ◽  
Anthocyanin Biosynthetic Pathway ◽  
Transparent Testa ◽  
Color Mutation ◽  
Mutant Flower

Abstract Background Roses are famous ornamental plants worldwide. Floral coloration is one of the most prominent traits in roses and is mainly regulated through the anthocyanin biosynthetic pathway. In this study, we investigated the key genes and metabolites of the anthocyanin biosynthetic pathway involved in color mutation in miniature roses. A comparative metabolome and transcriptome analysis was carried out on the Neptune King rose and its color mutant, Queen rose, at the blooming stage. Neptune King rose has light pink colored petals while Queen rose has deep pink colored petals. Result A total of 190 flavonoid-related metabolites and 38,551 unique genes were identified. The contents of 45 flavonoid-related metabolites, and the expression of 15 genes participating in the flavonoid pathway, varied significantly between the two cultivars. Seven anthocyanins (cyanidin 3-O-glucosyl-malonylglucoside, cyanidin O-syringic acid, cyanidin 3-O-rutinoside, cyanidin 3-O-galactoside, cyanidin 3-O-glucoside, peonidin 3-O-glucoside chloride, and pelargonidin 3-O-glucoside) were found to be the major metabolites, with higher abundance in the Queen rose. Thirteen anthocyanin biosynthetic related genes showed an upregulation trend in the mutant flower, which may favor the higher levels of anthocyanins in the mutant. Besides, eight TRANSPARENT TESTA 12 genes were found upregulated in Queen rose, probably contributing to a high vacuolar sequestration of anthocyanins. Thirty transcription factors, including two MYB and one bHLH, were differentially expressed between the two cultivars. Conclusions This study provides important insights into major genes and metabolites of the anthocyanin biosynthetic pathway modulating flower coloration in miniature rose. The results will be conducive for manipulating the anthocyanin pathways in order to engineer novel miniature rose cultivars with specific colors.

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.

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