scholarly journals Transcriptome analysis and identification of key genes involved in 1-deoxynojirimycin biosynthesis of mulberry (Morus alba L.)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5443 ◽  
Author(s):  
Dujun Wang ◽  
Li Zhao ◽  
Dan Wang ◽  
Jia Liu ◽  
Xiaofeng Yu ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
De Novo ◽  
Amine Oxidase ◽  
Average Length ◽  
Morus Alba ◽  
Cdna Libraries ◽  
Alkaloid Biosynthesis ◽  
Mulberry Leaf ◽  
Primary Amine Oxidase ◽  
Key Genes

Mulberry (Morus alba L.) represents one of the most commonly utilized plants in traditional medicine and as a nutritional plant used worldwide. The polyhydroxylated alkaloid 1-deoxynojirimycin (DNJ) is the major bioactive compounds of mulberry in treating diabetes. However, the DNJ content in mulberry is very low. Therefore, identification of key genes involved in DNJ alkaloid biosynthesis will provide a basis for the further analysis of its biosynthetic pathway and ultimately for the realization of synthetic biological production. Here, two cDNA libraries of mulberry leaf samples with different DNJ contents were constructed. Approximately 16 Gb raw RNA-Seq data was generated and de novo assembled into 112,481 transcripts, with an average length of 766 bp and an N50 value of 1,392. Subsequently, all unigenes were annotated based on nine public databases; 11,318 transcripts were found to be significantly differentially regulated. A total of 38 unique candidate genes were identified as being involved in DNJ alkaloid biosynthesis in mulberry, and nine unique genes had significantly different expression. Three key transcripts of DNJ biosynthesis were identified and further characterized using RT-PCR; they were assigned to lysine decarboxylase and primary-amine oxidase genes. Five CYP450 transcripts and two methyltransferase transcripts were significantly associated with DNJ content. Overall, the biosynthetic pathway of DNJ alkaloid was preliminarily speculated.

scholarly journals Transcriptome Analysis of Ramie (Boehmeria niveaL. Gaud.) in Response to Ramie Moth (Cocytodes coeruleaGuenée) Infestation

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Liangbin Zeng ◽  
Airong Shen ◽  
Jia Chen ◽  
Zhun Yan ◽  
Touming Liu ◽  
...  
Keyword(s):  
Protein Function ◽  
Molecular Mechanisms ◽  
Defense Mechanism ◽  
Natural Fiber ◽  
De Novo ◽  
Average Length ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Cdna Libraries ◽  
Pcr Analysis

The ramie mothCocytodes coeruleaGuenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore,de novoassembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

scholarly journals Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)

Genome ◽  
2018 ◽  
Vol 61 (6) ◽  
pp. 417-428 ◽  
Author(s):  
Shruti Choudhary ◽  
Sapna Thakur ◽  
Raoof Ahmad Najar ◽  
Aasim Majeed ◽  
Amandeep Singh ◽  
...  
Keyword(s):  
De Novo ◽  
Average Length ◽  
Cdna Libraries ◽  
High Quality ◽  
Single Nucleotide ◽  
Rhododendron Arboreum ◽  
Functional Annotations ◽  
Gene Ontology Database ◽  
Functional Aspects ◽  
Polymorphic Variants

Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina’s platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710 were grouped into 141 pathways and 23 746 encoded for different transcription factors. Transcriptome screening further identified 35 419 microsatellite regions, of which, 43 polymorphic loci were characterized on 30 genotypes. Seven hundred and nineteen transcripts had 811 high-quality single-nucleotide polymorphic variants with a minimum coverage of 10, a total score of 20, and SNP% of 50.

scholarly journals De novo transcriptome sequence of Senna tora provides insights into anthraquinone biosynthesis

2019 ◽  
Author(s):  
Sang-Ho Kang ◽  
Woo-Haeng Lee ◽  
Chang-Muk Lee ◽  
Joon-Soo Sim ◽  
So Youn Won ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Regulatory Mechanism ◽  
De Novo ◽  
Differential Expression Analysis ◽  
Rna Seq ◽  
De Novo Transcriptome ◽  
Secondary Metabolite Biosynthesis ◽  
Long Read ◽  
Annual Herb ◽  
Key Genes

AbstractSenna tora is an annual herb with rich source of anthraquinones that have tremendous pharmacological properties. However, there is little mention of genetic information for this species, especially regarding the biosynthetic pathways of anthraquinones. To understand the key genes and regulatory mechanism of anthraquinone biosynthesis pathways, we performed spatial and temporal transcriptome sequencing of S. tora using short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) technologies, and generated two unigene sets composed of 118,635 and 39,364, respectively. A comprehensive functional annotation and classification with multiple public databases identified array of genes involved in major secondary metabolite biosynthesis pathways and important transcription factor (TF) families (MYB, MYB-related, AP2/ERF, C2C2-YABBY, and bHLH). Differential expression analysis indicated that the expression level of genes involved in anthraquinone biosynthetic pathway regulates differently depending on the degree of tissues and seeds development. Furthermore, we identified that the amount of anthraquinone compounds were greater in late seeds than early ones. In conclusion, these results provide a rich resource for understanding the anthraquinone metabolism in S. tora.

scholarly journals Transcriptome analyses provide insights into the difference of alkaloids biosynthesis in the Chinese goldthread (Coptis chinensis Franch.) from different biotopes

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3303 ◽  
Author(s):  
Hanting Chen ◽  
Cao Deng ◽  
Hu Nie ◽  
Gang Fan ◽  
Yang He
Keyword(s):  
De Novo ◽  
Amine Oxidase ◽  
Chemical Components ◽  
Sequencing Data ◽  
Coptis Chinensis ◽  
Coding Regions ◽  
Eukaryotic Genes ◽  
Primary Amine Oxidase ◽  
The Difference

Coptis chinensis Franch., the Chinese goldthread (‘Weilian’ in Chinese), one of the most important medicinal plants from the family Ranunculaceae, and its rhizome has been widely used in Traditional Chinese Medicine for centuries. Here, we analyzed the chemical components and the transcriptome of the Chinese goldthread from three biotopes, including Zhenping, Zunyi and Shizhu. We built comprehensive, high-quality de novo transcriptome assemblies of the Chinese goldthread from short-read RNA-Sequencing data, obtaining 155,710 transcripts and 56,071 unigenes. More than 98.39% and 95.97% of core eukaryotic genes were found in the transcripts and unigenes respectively, indicating that this unigene set capture the majority of the coding genes. A total of 520,462, 493,718, and 507,247 heterozygous SNPs were identified in the three accessions from Zhenping, Zunyi, and Shizhu respectively, indicating high polymorphism in coding regions of the Chinese goldthread (∼1%). Chemical analyses of the rhizome identified six major components, including berberine, palmatine, coptisine, epiberberine, columbamine, and jatrorrhizine. Berberine has the highest concentrations, followed by coptisine, palmatine, and epiberberine sequentially for all the three accessions. The drug quality of the accession from Shizhu may be the highest among these accessions. Differential analyses of the transcriptome identified four pivotal candidate enzymes, including aspartate aminotransferaseprotein, polyphenol oxidase, primary-amine oxidase, and tyrosine decarboxylase, were significantly differentially expressed and may be responsible for the difference of alkaloids contents in the accessions from different biotopes.

Tropane alkaloid biosynthesis: a centennial review

2021 ◽  
Author(s):  
Jian-Ping Huang ◽  
Yong-Jiang Wang ◽  
Tian Tian ◽  
Li Wang ◽  
Yijun Yan ◽  
...  
Keyword(s):  
De Novo ◽  
Tropane Alkaloid ◽  
Alkaloid Biosynthesis

From the first ambitious imagination of tropinone biosynthesis mechanism in plants published in 1917 to the de novo production of scopolamine in yeast realized in 2020, what did we learn from this long story of more than 100 years old?

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.

scholarly journals Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)

Biology ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 36
Author(s):  
Te-Hua Hsu ◽  
Yu-Ting Chiu ◽  
Hung-Tai Lee ◽  
Hong-Yi Gong ◽  
Chang-Wen Huang
Keyword(s):  
Molecular Markers ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Growth Traits ◽  
Gene Diversity ◽  
Snp Markers ◽  
Cdna Libraries ◽  
Functional Markers ◽  
Genetic Management ◽  
Ssr And Snp Markers

The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.

scholarly journals Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 189
Author(s):  
Kinga Kęska ◽  
Michał Wojciech Szcześniak ◽  
Izabela Makałowska ◽  
Małgorzata Czernicka
Keyword(s):  
Stress Tolerance ◽  
De Novo ◽  
Average Length ◽  
Marker Genes ◽  
Long Term Memory ◽  
Low Oxygen ◽  
Waterlogging Tolerance ◽  
Pre Treatment ◽  
Waterlogging Treatment

Waterlogging (WL), excess water in the soil, is a phenomenon often occurring during plant cultivation causing low oxygen levels (hypoxia) in the soil. The aim of this study was to identify candidate genes involved in long-term waterlogging tolerance in cucumber using RNA sequencing. Here, we also determined how waterlogging pre-treatment (priming) influenced long-term memory in WL tolerant (WL-T) and WL sensitive (WL-S) i.e., DH2 and DH4 accessions, respectively. This work uncovered various differentially expressed genes (DEGs) activated in the long-term recovery in both accessions. De novo assembly generated 36,712 transcripts with an average length of 2236 bp. The results revealed that long-term waterlogging had divergent impacts on gene expression in WL-T DH2 and WL-S DH4 cucumber accessions: after 7 days of waterlogging, more DEGs in comparison to control conditions were identified in WL-S DH4 (8927) than in WL-T DH2 (5957). Additionally, 11,619 and 5007 DEGs were identified after a second waterlogging treatment in the WL-S and WL-T accessions, respectively. We identified genes associated with WL in cucumber that were especially related to enhanced glycolysis, adventitious roots development, and amino acid metabolism. qRT-PCR assay for hypoxia marker genes i.e., alcohol dehydrogenase (adh), 1-aminocyclopropane-1-carboxylate oxidase (aco) and long chain acyl-CoA synthetase 6 (lacs6) confirmed differences in response to waterlogging stress between sensitive and tolerant cucumbers and effectiveness of priming to enhance stress tolerance.

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