scholarly journals Effective prediction of biosynthetic pathway genes involved in bioactive polyphyllins in Paris polyphylla

2022 ◽  
Vol 5 (1) ◽  
Author(s):  
Xin Hua ◽  
Wei Song ◽  
Kangzong Wang ◽  
Xue Yin ◽  
Changqi Hao ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Biosynthetic Pathway ◽  
Tissue Specificity ◽  
Cytochrome P450s ◽  
Oxidosqualene Cyclases ◽  
Third Generation Sequencing ◽  
Paris Polyphylla ◽  
Key Genes ◽  
Sequencing Platforms ◽  
Generation Sequencing

AbstractThe genes in polyphyllins pathway mixed with other steroid biosynthetic genes form an extremely complex biosynthetic network in Paris polyphylla with a giant genome. The lack of genomic data and tissue specificity causes the study of the biosynthetic pathway notably difficult. Here, we report an effective method for the prediction of key genes of polyphyllin biosynthesis. Full-length transcriptome from eight different organs via hybrid sequencing of next generation sequencingand third generation sequencing platforms annotated two 2,3-oxidosqualene cyclases (OSCs), 216 cytochrome P450s (CYPs), and 199 UDP glycosyltransferases (UGTs). Combining metabolic differences, gene-weighted co-expression network analysis, and phylogenetic trees, the candidate ranges of OSC, CYP, and UGT genes were further narrowed down to 2, 15, and 24, respectively. Beside the three previously characterized CYPs, we identified the OSC involved in the synthesis of cycloartenol and the UGT (PpUGT73CR1) at the C-3 position of diosgenin and pennogenin in P. polyphylla. This study provides an idea for the investigation of gene cluster deficiency biosynthesis pathways in medicinal plants.

scholarly journals Coupling Comprehensive Transcriptome-Metabolome Association and Phylogenetic Analysis Speed Dissecion of Polyphyllins Biosynthetic Pathway

2021 ◽  
Author(s):  
Xin Hua ◽  
Wei Song ◽  
Kangzong Wang ◽  
Xue Yin ◽  
Changqi Hao ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Biosynthetic Pathway ◽  
Tissue Specificity ◽  
Herbaceous Plant ◽  
Illumina Platform ◽  
Metabolic Analysis ◽  
Paris Polyphylla ◽  
Key Genes ◽  
First Time ◽  
Group D

AbstractParis polyphylla var. yunnanensis is an endangered herbaceous plant accumulating polyphyllins, which are widely used in clinical treatment in China. The genes involved in the biosynthesis of polyphyllins are often mixed with other steroids biosynthetic genes, forming a very complex biosynthetic network. The lack of genomic data and tissue specificity of genes makes it extremely difficult to study the biosynthetic pathway of polyphyllins. Here we report an effective method for predicting key genes of polyphyllins biosynthesis. Eight different organs were selected for metabolic analysis and transcriptome sequencing using both of PacBio and Illumina platform generating a total of 370 G of pure data, and two OSCs, 216 CYPs, and 199 UGTs were annotated. By constructing phylogenetic trees, we screened out 60 and 57 candidate genes in the CYP72, CYP90, CYP94 families of CYPs and group D of UGTs, respectively. Metabolic analysis indicates cholesterol, diosgenin, and polyphyllins et al. key metabolites varied in different selected oragns. Three modules were identified by metabolite and gene weighted co-expression network analysis, from which 41 candidate CYPs and 47 candidate UGTs were identified. Combined above information, we narrowed the candidate range of OSC, CYP and UGT genes to 2, 15 and 20. Beside three previous characterized CYPs, we also identified the OSC involved in the synthesis of diosgenin and the glycosyltransferase at the C-3 position of diosgenin for the first time in P. polyphylla. This study provides a new idea for the study of gene cluster deficiency biosynthesis pathways in medicinal plants.

scholarly journals Transcriptome-wide survey of pseudorabies virus using next- and third-generation sequencing platforms

2018 ◽  
Vol 5 (1) ◽  
Author(s):  
Dóra Tombácz ◽  
Donald Sharon ◽  
Attila Szűcs ◽  
Norbert Moldován ◽  
Michael Snyder ◽  
...  
Keyword(s):  
Pseudorabies Virus ◽  
Third Generation ◽  
Third Generation Sequencing ◽  
Sequencing Platforms ◽  
Generation Sequencing

scholarly journals Versatile Quality Control Methods for Nanopore Sequencing

2019 ◽  
Vol 15 ◽  
pp. 117693431986306
Author(s):  
Davide Bolognini ◽  
Roberto Semeraro ◽  
Alberto Magi
Keyword(s):  
Quality Control ◽  
Control Method ◽  
Nanopore Sequencing ◽  
Control Methods ◽  
Sequencing Data ◽  
Third Generation Sequencing ◽  
Quality Control Method ◽  
Sequencing Platforms ◽  
Generation Sequencing

Third-generation sequencing using nanopores as biosensors has recently emerged as a strategy capable to overcome next-generation sequencing drawbacks and pitfalls. Assessing the quality of the data produced by nanopore sequencing platforms is essential to decide how useful these may be in making biological discoveries. Here, we briefly contextualized NanoR, a quality control method for nanopore sequencing data we developed, in the scenario of preexistent similar tools. We also illustrated 2 quality control pipelines, readily applicable to nanopore sequencing data, respectively, based on NanoR and PyPore, a second quality control method published by our group.

BUILDING CATALOGUE OF LIFE: ULTRAHIGH THROUGHPUT DNA BARCODING USING THIRD GENERATION SEQUENCING

2018 ◽  
Author(s):  
P.D.N. HEBERT ◽  
◽  
T.W.A. BRAUKMANN ◽  
S.W.J. PROSSER ◽  
S. RATNASINGHAM ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Third Generation ◽  
Third Generation Sequencing ◽  
Generation Sequencing

IsoDetect: Detection of splice isoforms from third generation long reads based on short feature sequences

2020 ◽  
Vol 15 ◽  
Author(s):  
Hongdong Li ◽  
Wenjing Zhang ◽  
Yuwen Luo ◽  
Jianxin Wang
Keyword(s):  
Sequence Similarity ◽  
Detection Methods ◽  
Sequence Information ◽  
Third Generation ◽  
Sequencing Data ◽  
Splice Isoforms ◽  
Third Generation Sequencing ◽  
Long Reads ◽  
Feature Sequence ◽  
Generation Sequencing

Aims: Accurately detect isoforms from third generation sequencing data. Background: Transcriptome annotation is the basis for the analysis of gene expression and regulation. The transcriptome annotation of many organisms such as humans is far from incomplete, due partly to the challenge in the identification of isoforms that are produced from the same gene through alternative splicing. Third generation sequencing (TGS) reads provide unprecedented opportunity for detecting isoforms due to their long length that exceeds the length of most isoforms. One limitation of current TGS reads-based isoform detection methods is that they are exclusively based on sequence reads, without incorporating the sequence information of known isoforms. Objective: Develop an efficient method for isoform detection. Method: Based on annotated isoforms, we propose a splice isoform detection method called IsoDetect. First, the sequence at exon-exon junction is extracted from annotated isoforms as the “short feature sequence”, which is used to distinguish different splice isoforms. Second, we aligned these feature sequences to long reads and divided long reads into groups that contain the same set of feature sequences, thereby avoiding the pair-wise comparison among the large number of long reads. Third, clustering and consensus generation are carried out based on sequence similarity. For the long reads that do not contain any short feature sequence, clustering analysis based on sequence similarity is performed to identify isoforms. Result: Tested on two datasets from Calypte Anna and Zebra Finch, IsoDetect showed higher speed and compelling accuracy compared with four existing methods. Conclusion: IsoDetect is a promising method for isoform detection. Other: This paper was accepted by the CBC2019 conference.

Enzymatic dimerization in the biosynthetic pathway of microbial natural products

2021 ◽  
Author(s):  
Jiawang Liu ◽  
Anan Liu ◽  
Youcai Hu
Keyword(s):  
Natural Products ◽  
Biosynthetic Pathway ◽  
Structural Diversity ◽  
Cytochrome P450s ◽  
Microbial Natural Products

Cytochrome P450s, laccases, and intermolecular [4 + 2] cyclases, along with other enzymes were utilized to catalyze varied dimerization of matured natural products so as to create the structural diversity and complexity in microorganisms.

scholarly journals Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Anzhen Fu ◽  
Qing Wang ◽  
Jianlou Mu ◽  
Lili Ma ◽  
Changlong Wen ◽  
...  
Keyword(s):  
Fruit Development ◽  
Repetitive Sequences ◽  
Genetic Research ◽  
Future Research ◽  
Agricultural Crop ◽  
Protein Coding ◽  
Third Generation Sequencing ◽  
Sechium Edule ◽  
Generation Sequencing ◽  
Cucurbitaceae Family

AbstractChayote (Sechium edule) is an agricultural crop in the Cucurbitaceae family that is rich in bioactive components. To enhance genetic research on chayote, we used Nanopore third-generation sequencing combined with Hi–C data to assemble a draft chayote genome. A chromosome-level assembly anchored on 14 chromosomes (N50 contig and scaffold sizes of 8.40 and 46.56 Mb, respectively) estimated the genome size as 606.42 Mb, which is large for the Cucurbitaceae, with 65.94% (401.08 Mb) of the genome comprising repetitive sequences; 28,237 protein-coding genes were predicted. Comparative genome analysis indicated that chayote and snake gourd diverged from sponge gourd and that a whole-genome duplication (WGD) event occurred in chayote at 25 ± 4 Mya. Transcriptional and metabolic analysis revealed genes involved in fruit texture, pigment, flavor, flavonoids, antioxidants, and plant hormones during chayote fruit development. The analysis of the genome, transcriptome, and metabolome provides insights into chayote evolution and lays the groundwork for future research on fruit and tuber development and genetic improvements in chayote.

scholarly journals Transcriptome and Metabolome Dynamics Explain Aroma Differences between Green and Red Prickly Ash Fruit

Foods ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 391
Author(s):  
Xitong Fei ◽  
Yichen Qi ◽  
Yu Lei ◽  
Shujie Wang ◽  
Haichao Hu ◽  
...  
Keyword(s):  
Redundancy Analysis ◽  
Biosynthetic Pathway ◽  
Expression Patterns ◽  
Gas Chromatography Mass Spectrometry ◽  
Zanthoxylum Armatum ◽  
Aroma Characteristics ◽  
Main Factors ◽  
Key Genes ◽  
Zanthoxylum Bungeanum ◽  
Aroma Components

Green prickly ash (Zanthoxylum armatum) and red prickly ash (Zanthoxylum bungeanum) fruit have unique flavor and aroma characteristics that affect consumers’ purchasing preferences. However, differences in aroma components and relevant biosynthesis genes have not been systematically investigated in green and red prickly ash. Here, through the analysis of differentially expressed genes (DEGs), differentially abundant metabolites, and terpenoid biosynthetic pathways, we characterize the different aroma components of green and red prickly ash fruits and identify key genes in the terpenoid biosynthetic pathway. Gas chromatography-mass spectrometry (GC-MS) was used to identify 41 terpenoids from green prickly ash and 61 terpenoids from red prickly ash. Piperitone was the most abundant terpenoid in green prickly ash fruit, whereas limonene was most abundant in red prickly ash. Intergroup correlation analysis and redundancy analysis showed that HDS2, MVK2, and MVD are key genes for terpenoid synthesis in green prickly ash, whereas FDPS2 and FDPS3 play an important role in the terpenoid synthesis of red prickly ash. In summary, differences in the composition and content of terpenoids are the main factors that cause differences in the aromas of green and red prickly ash, and these differences reflect contrasting expression patterns of terpenoid synthesis genes.

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