scholarly journals Triterpenoid Saponin Biosynthetic Pathway Profiling and Candidate Gene Mining of the Ilex asprella Root Using RNA-Seq

2014 ◽  
Vol 15 (4) ◽  
pp. 5970-5987 ◽  
Author(s):  
Xiasheng Zheng ◽  
Hui Xu ◽  
Xinye Ma ◽  
Ruoting Zhan ◽  
Weiwen Chen
Keyword(s):  
Candidate Gene ◽  
Biosynthetic Pathway ◽  
Triterpenoid Saponin ◽  
Rna Seq ◽  
Gene Mining

scholarly journals A candidate gene identified in converting platycoside E to platycodin D from Platycodon grandiflorus by transcriptome and main metabolites analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xinglong Su ◽  
Yingying Liu ◽  
Lu Han ◽  
Zhaojian Wang ◽  
Mengyang Cao ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Orthogonal Experiment ◽  
Triterpenoid Saponin ◽  
Gene Encoding ◽  
Triterpenoid Saponins ◽  
Platycodin D ◽  
Polysaccharide Content ◽  
Saponin Biosynthesis ◽  
Polysaccharide Synthesis ◽  
Experimental Use

AbstractPlatycodin D and platycoside E are two triterpenoid saponins in Platycodon grandiflorus, differing only by two glycosyl groups structurally. Studies have shown β-Glucosidase from bacteria can convert platycoside E to platycodin D, indicating the potential existence of similar enzymes in P. grandiflorus. An L9(34) orthogonal experiment was performed to establish a protocol for calli induction as follows: the optimal explant is stems with nodes and the optimum medium formula is MS + NAA 1.0 mg/L + 6-BA 0.5 mg/L to obtain callus for experimental use. The platycodin D, platycoside E and total polysaccharides content between callus and plant organs varied wildly. Platycodin D and total polysaccharide content of calli was found higher than that of leaves. While, platycoside E and total polysaccharide content of calli was found lower than that of leaves. Associating platycodin D and platycoside E content with the expression level of genes involved in triterpenoid saponin biosynthesis between calli and leaves, three contigs were screened as putative sequences of β-Glucosidase gene converting platycoside E to platycodin D. Besides, we inferred that some transcription factors can regulate the expression of key enzymes involved in triterpernoid saponins and polysaccharides biosynthesis pathway of P. grandiflorus. Totally, a candidate gene encoding enzyme involved in converting platycoside E to platycodin D, and putative genes involved in polysaccharide synthesis in P. grandiflorus had been identified. This study will help uncover the molecular mechanism of triterpenoid saponins biosynthesis in P. grandiflorus.

scholarly journals Meta-analysis of soybean amino acid QTLs and candidate gene mining

2018 ◽  
Vol 17 (5) ◽  
pp. 1074-1084 ◽  
Author(s):  
Qian-chun GONG ◽  
Hong-xiao YU ◽  
Xin-rui MAO ◽  
Hui-dong QI ◽  
Yan SHI ◽  
...  
Keyword(s):  
Amino Acid ◽  
Candidate Gene ◽  
Meta Analysis ◽  
Gene Mining

scholarly journals Meta-analysis and candidate gene mining of low-phosphorus tolerance in maize

2014 ◽  
Vol 56 (3) ◽  
pp. 262-270 ◽  
Author(s):  
Hongwei Zhang ◽  
Mohammed Shalim Uddin ◽  
Cheng Zou ◽  
Chuanxiao Xie ◽  
Yunbi Xu ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Meta Analysis ◽  
Gene Mining ◽  
Low Phosphorus ◽  
Low Phosphorus Tolerance

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 The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat

2020 ◽  
Vol 10 (10) ◽  
pp. 3675-3686 ◽  
Author(s):  
Sophie A. Harrington ◽  
Anna E. Backhaus ◽  
Ajit Singh ◽  
Keywan Hassani-Pak ◽  
Cristobal Uauy
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Candidate Gene ◽  
Web Application ◽  
Regulatory Networks ◽  
Target Genes ◽  
Gene Prediction ◽  
Relevant Information ◽  
Rna Seq ◽  
Biologically Relevant

Gene regulatory networks are powerful tools which facilitate hypothesis generation and candidate gene discovery. However, the extent to which the network predictions are biologically relevant is often unclear. Recently a GENIE3 network which predicted targets of wheat transcription factors was produced. Here we used an independent RNA-Seq dataset to test the predictions of the wheat GENIE3 network for the senescence-regulating transcription factor NAM-A1 (TraesCS6A02G108300). We re-analyzed the RNA-Seq data against the RefSeqv1.0 genome and identified a set of differentially expressed genes (DEGs) between the wild-type and nam-a1 mutant which recapitulated the known role of NAM-A1 in senescence and nutrient remobilisation. We found that the GENIE3-predicted target genes of NAM-A1 overlap significantly with the DEGs, more than would be expected by chance. Based on high levels of overlap between GENIE3-predicted target genes and the DEGs, we identified candidate senescence regulators. We then explored genome-wide trends in the network related to polyploidy and found that only homeologous transcription factors are likely to share predicted targets in common. However, homeologs which vary in expression levels across tissues are less likely to share predicted targets than those that do not, suggesting that they may be more likely to act in distinct pathways. This work demonstrates that the wheat GENIE3 network can provide biologically-relevant predictions of transcription factor targets, which can be used for candidate gene prediction and for global analyses of transcription factor function. The GENIE3 network has now been integrated into the KnetMiner web application, facilitating its use in future studies.

scholarly journals In silico candidate gene mining in livestock species

2007 ◽  
Vol 6 (sup1) ◽  
pp. 217-217
Author(s):  
A. Stella ◽  
A. Montironi ◽  
F. Panzitta ◽  
G. Gandini ◽  
P. J. Boettcher
Keyword(s):  
Candidate Gene ◽  
In Silico ◽  
Livestock Species ◽  
Gene Mining
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