scholarly journals De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

2020 ◽  
Author(s):  
Guolin Zhou ◽  
Ping Zhu
Keyword(s):  
Secondary Metabolites ◽  
Transcriptome Sequencing ◽  
De Novo ◽  
Illumina Hiseq ◽  
Medicinal Value ◽  
Relieve Pain ◽  
Chemical Studies ◽  
Illumina Hiseq Platform ◽  
Differential Gene ◽  
First Time

Abstract Background: Rhododendron molle (Ericaceae) is a traditional Chinese medicinal plant, its flower and root have been widely used to treat rheumatism and relieve pain for thousands of years in China. Chemical studies have revealed that R. molle contains abundant secondary metabolites such as terpenoinds, flavonoids and lignans, some of which have exhibited various bioactivities including antioxidant, hypotension and analgesic activity. In spite of immense pharmaceutical importance, the mechanism underlying the biosynthesis of secondary metabolites remains unknown and the genomic information is unavailable. Results: To gain molecular insight into this plant, especially on the information of pharmaceutically important secondary metabolites including grayanane diterpenoids, we conducted deep transcriptome sequencing for R. molle flower and root using the Illumina Hiseq platform. In total, 100,603 unigenes were generated through de novo assembly with mean length of 778 bp, 57.1% of these unigenes were annotated in public databases and 17,906 of those unigenes showed significant match in the KEGG database. Unigenes involved in the biosynthesis of secondary metabolites were annotated, including the TPSs and CYPs that were potentially responsible for the biosynthesis of grayanoids. Moreover, 3,376 transcription factors and 10,828 simple sequence repeats (SSRs) were also identified. Additionally, we further performed differential gene expression (DEG) analysis of the flower and root transcriptome libraries and identified numerous genes that were specifically expressed or up-regulated in flower.Conclusions: To the best of our knowledge, this is the first time to generate and thoroughly analyze the transcriptome data of both R. molle flower and root. This study provided an important genetic resource which will shed light on elucidating various secondary metabolite biosynthetic pathways in R. molle, especially for those with medicinal value and allow for drug development in this plant.

scholarly journals De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

2020 ◽  
Author(s):  
Guolin Zhou ◽  
Ping Zhu
Keyword(s):  
Secondary Metabolites ◽  
Transcriptome Sequencing ◽  
De Novo ◽  
Illumina Hiseq ◽  
Medicinal Value ◽  
Relieve Pain ◽  
Chemical Studies ◽  
Illumina Hiseq Platform ◽  
Differential Gene ◽  
First Time

Abstract Background: Rhododendron molle (Ericaceae) is a traditional Chinese medicinal plant, its flower and root have been widely used to treat rheumatism and relieve pain for thousands of years in China. Chemical studies have revealed that R. molle contains abundant secondary metabolites such as terpenoinds, flavonoids and lignans, some of which have exhibited various bioactivities including antioxidant, hypotension and analgesic activity. In spite of immense pharmaceutical importance, the mechanism underlying the biosynthesis of secondary metabolites remains unknown and the genomic information is unavailable. Results: To gain molecular insight into this plant, especially on the pharmaceutically important secondary metabolic information, we conducted deep transcriptome sequencing for R. molle flower and root using the Illumina Hiseq platform. In total, 100,603 unigenes were generated through de novo assembly with mean length of 778 bp, 57.1% of these unigenes were annotated in public databases and 17,906 of those unigenes showed significant match in the KEGG database. Unigenes involved in the biosynthesis of secondary metabolites were annotated, including the TPSs and CYPs that were potentially responsible for the biosynthesis of grayanoids. Moreover, 3,376 transcription factors and 10,828 simple sequence repeats (SSRs) were also identified. Additionally, we further performed differential gene expression (DEG) analysis of the flower and root transcriptome libraries and identified numerous genes that were specifically expressed or up-regulated in flower.Conclusions: To the best of our knowledge, this is the first time to generate and thoroughly analyze the transcriptome data of both R. molle flower and root. This study provided an important genetic resource which will shed light on elucidating various secondary metabolite biosynthetic pathways in R. molle, especially for those with medicinal value and allow for drug development in this plant.

scholarly journals De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

2019 ◽  
Author(s):  
Guolin Zhou ◽  
Ping Zhu
Keyword(s):  
Secondary Metabolites ◽  
Transcriptome Sequencing ◽  
De Novo ◽  
Illumina Hiseq ◽  
Medicinal Value ◽  
Relieve Pain ◽  
Chemical Studies ◽  
Illumina Hiseq Platform ◽  
Differential Gene ◽  
First Time

Abstract Background Rhododendron molle (Ericaceae) is a traditional Chinese medicinal plant, its flower and root have been widely used to treat rheumatism and relieve pain for thousands of years in China. Chemical studies have revealed that R. molle contains abundant secondary metabolites such as terpenoinds, flavonoids and lignans, some of which have exhibited various bioactivities including analgesia and hypotension. In despite of immense pharmaceutical importance, the mechanism underlying the biosynthesis of secondary metabolites remains unknown and the genomic information is unavailable.Results To gain molecular insight into the R. molle , we conducted deep transcriptome sequencing for R. molle flower and root using the Illumina Hiseq platform. In total, 100,603 unigenes were generated through de novo assembly with mean length of 778 bp, 57.1% of these unigenes were annotated in public databases and 17,906 of those unigenes showed significant match in the KEGG database. Unigenes involved in biosynthesis of secondary metabolites were annotated. Moreover, 3,376 transcription factors and 10,828 simple sequence repeats (SSRs) were also identified. Additionally, we further performed differential gene expression (DEG) analysis of the flower and root transcriptome libraries and identified numerous genes that were specifically expressed or up-regulated in flower.Conclusions To the best of our knowledge, this is the first time to generate and thoroughly analyze the transcriptome data of both R. molle flower and root. This study provided an important genetic resource which will shed light on elucidating various secondary metabolite biosynthetic pathways in R. molle , especially for those with medicinal value and allow for drug development in this herb.

scholarly journals De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

2020 ◽  
Author(s):  
Guolin Zhou ◽  
Ping Zhu
Keyword(s):  
Secondary Metabolites ◽  
Transcriptome Sequencing ◽  
De Novo ◽  
Illumina Hiseq ◽  
Medicinal Value ◽  
Relieve Pain ◽  
Chemical Studies ◽  
Illumina Hiseq Platform ◽  
Differential Gene ◽  
First Time

Abstract Background: Rhododendron molle (Ericaceae) is a traditional Chinese medicinal plant, its flower and root have been widely used to treat rheumatism and relieve pain for thousands of years in China. Chemical studies have revealed that R. molle contains abundant secondary metabolites such as terpenoinds, flavonoids and lignans, some of which have exhibited various bioactivities including antioxidant, hypotension and analgesic activity. In spite of immense pharmaceutical importance, the mechanism underlying the biosynthesis of secondary metabolites remains unknown and the genomic information is unavailable. Results: To gain molecular insight into this plant, especially on the information of pharmaceutically important secondary metabolites including grayanane diterpenoids, we conducted deep transcriptome sequencing for R. molle flower and root using the Illumina Hiseq platform. In total, 100,603 unigenes were generated through de novo assembly with mean length of 778 bp, 57.1% of these unigenes were annotated in public databases and 17,906 of those unigenes showed significant match in the KEGG database. Unigenes involved in the biosynthesis of secondary metabolites were annotated, including the TPSs and CYPs that were potentially responsible for the biosynthesis of grayanoids. Moreover, 3,376 transcription factors and 10,828 simple sequence repeats (SSRs) were also identified. Additionally, we further performed differential gene expression (DEG) analysis of the flower and root transcriptome libraries and identified numerous genes that were specifically expressed or up-regulated in flower.Conclusions: To the best of our knowledge, this is the first time to generate and thoroughly analyze the transcriptome data of both R. molle flower and root. This study provided an important genetic resource which will shed light on elucidating various secondary metabolite biosynthetic pathways in R. molle, especially for those with medicinal value and allow for drug development in this plant.

scholarly journals De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

2020 ◽  
Author(s):  
Guolin Zhou ◽  
Ping Zhu
Keyword(s):  
Secondary Metabolites ◽  
Transcriptome Sequencing ◽  
De Novo ◽  
Illumina Hiseq ◽  
Medicinal Value ◽  
Relieve Pain ◽  
Chemical Studies ◽  
Illumina Hiseq Platform ◽  
Differential Gene ◽  
First Time

Abstract Background: Rhododendron molle (Ericaceae) is a traditional Chinese medicinal plant, its flower and root have been widely used to treat rheumatism and relieve pain for thousands of years in China. Chemical studies have revealed that R. molle contains abundant secondary metabolites such as terpenoinds, flavonoids and lignans, some of which have exhibited various bioactivities including antioxidant, hypotension and analgesic activity. In spite of immense pharmaceutical importance, the mechanism underlying the biosynthesis of secondary metabolites remains unknown and the genomic information is unavailable. Results: To gain molecular insight into this plant, especially on the information of pharmaceutically important secondary metabolites including grayanane diterpenoids, we conducted deep transcriptome sequencing for R. molle flower and root using the Illumina Hiseq platform. In total, 100,603 unigenes were generated through de novo assembly with mean length of 778 bp, 57.1% of these unigenes were annotated in public databases and 17,906 of those unigenes showed significant match in the KEGG database. Unigenes involved in the biosynthesis of secondary metabolites were annotated, including the TPSs and CYPs that were potentially responsible for the biosynthesis of grayanoids. Moreover, 3,376 transcription factors and 10,828 simple sequence repeats (SSRs) were also identified. Additionally, we further performed differential gene expression (DEG) analysis of the flower and root transcriptome libraries and identified numerous genes that were specifically expressed or up-regulated in flower.Conclusions: To the best of our knowledge, this is the first time to generate and thoroughly analyze the transcriptome data of both R. molle flower and root. This study provided an important genetic resource which will shed light on elucidating various secondary metabolite biosynthetic pathways in R. molle, especially for those with medicinal value and allow for drug development in this plant.

scholarly journals De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

2020 ◽  
Author(s):  
Guolin Zhou ◽  
Ping Zhu
Keyword(s):  
Secondary Metabolites ◽  
Transcriptome Sequencing ◽  
De Novo ◽  
Illumina Hiseq ◽  
Medicinal Value ◽  
Relieve Pain ◽  
Chemical Studies ◽  
Illumina Hiseq Platform ◽  
Differential Gene ◽  
First Time

Abstract Background: Rhododendron molle (Ericaceae) is a traditional Chinese medicinal plant, its flower and root have been widely used to treat rheumatism and relieve pain for thousands of years in China. Chemical studies have revealed that R. molle contains abundant secondary metabolites such as terpenoinds, flavonoids and lignans, some of which have exhibited various bioactivities including antioxidant, hypotension and analgesic activity. In spite of immense pharmaceutical importance, the mechanism underlying the biosynthesis of secondary metabolites remains unknown and the genomic information is unavailable. Results: To gain molecular insight into this plant, especially on the information of pharmaceutically important secondary metabolites including grayanane diterpenoids, we conducted deep transcriptome sequencing for R. molle flower and root using the Illumina Hiseq platform. In total, 100,603 unigenes were generated through de novo assembly with mean length of 778 bp, 57.1% of these unigenes were annotated in public databases and 17,906 of those unigenes showed significant match in the KEGG database. Unigenes involved in the biosynthesis of secondary metabolites were annotated, including the TPSs and CYPs that were potentially responsible for the biosynthesis of grayanoids. Moreover, 3,376 transcription factors and 10,828 simple sequence repeats (SSRs) were also identified. Additionally, we further performed differential gene expression (DEG) analysis of the flower and root transcriptome libraries and identified numerous genes that were specifically expressed or up-regulated in flower.Conclusions: To the best of our knowledge, this is the first time to generate and thoroughly analyze the transcriptome data of both R. molle flower and root. This study provided an important genetic resource which will shed light on elucidating various secondary metabolite biosynthetic pathways in R. molle, especially for those with medicinal value and allow for drug development in this plant.

scholarly journals Enhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues

2019 ◽  
Author(s):  
Shifeng Cheng ◽  
Yuan Fu ◽  
Yaolei Zhang ◽  
Wenfei Xian ◽  
Hongli Wang ◽  
...  
Keyword(s):  
Genome Size ◽  
Mongolian Gerbil ◽  
Transcriptome Sequencing ◽  
De Novo ◽  
Model Organism ◽  
Meriones Unguiculatus ◽  
Transcriptome Data ◽  
Illumina Hiseq ◽  
Tissue Samples ◽  
Different Tissues

Abstract BACKGROUND: The Mongolian gerbil (Meriones unguiculatus) has historically been used as a model organism for the auditory and visual systems, stroke/ischemia, epilepsy and aging related research since 1935 when laboratory gerbils were separated from their wild counterparts. In this study we report genome sequencing, assembly, and annotation further supported by transcriptome sequencing and assembly from 27 different tissues samples. RESULTS: The genome was assembled using Illumina HiSeq 2000 and resulted in a final genome size of 2.54 Gbp with contig and scaffold N50 values of 31.4 Kbp and 500.0 Kbp, respectively. Based on the k-mer estimated genome size of 2.48 Gbp, the assembly appears to be complete. The genome annotation was supported by transcriptome data that identified 31 769 (>2000bp) predicted protein-coding genes across 27 tissue samples. A BUSCO search of 3023 mammalian groups resulted in 86% of curated single copy orthologs present among predicted genes, indicating a high level of completeness of the genome. CONCLUSIONS: We report a de novo assembly of the Mongolian gerbil genome that was further enhanced by assembly of transcriptome data from several tissues. Sequencing of this genome increases the utility of the gerbil as a model organism, opening the availability of now widely used genetic tools.

scholarly journals Insights into the Gryllus bimaculatus Immune-Related Transcriptomic Profiling to Combat Naturally Invading Pathogens

2020 ◽  
Vol 6 (4) ◽  
pp. 232 ◽  
Author(s):  
Abid Hussain ◽  
Muhammad Waqar Ali ◽  
Ahmed Mohammed AlJabr ◽  
Saad Naser AL-Kahtani
Keyword(s):  
Defense Mechanism ◽  
Immune Defense ◽  
Cdna Libraries ◽  
Gryllus Bimaculatus ◽  
Illumina Hiseq ◽  
Field Crickets ◽  
Wide Range ◽  
Illumina Hiseq Platform ◽  
Immune Related Genes ◽  
First Time

Natural pathogen pressure is an important factor that shapes the host immune defense mechanism. The current study primarily aimed to explore the molecular basis of the natural immune defense mechanism of a sporadic pest, Gryllus bimaculatus, during swarming by constructing cDNA libraries of the female mid-gut, male mid-gut, testes, and ovaries. The Illumina HiSeq platform generated an average of 7.9 G, 11.77 G, 10.07 G, and 10.07 G bases of outputs from the male mid-gut, female mid-gut, testes, and ovaries and libraries, respectively. The transcriptome of two-spotted field crickets was assembled into 233,172 UniGenes, which yielded approximately 163.58 million reads. On the other hand, there were 43,055 genes in common that were shared among all the biological samples. Gene Ontology analysis successfully annotated 492 immune-related genes, which comprised mainly Pattern Recognition Receptors (62 genes), Signal modulators (57 genes), Signal transduction (214 genes), Effectors (36 genes), and another immune-related 123 genes. In summary, the identified wide range of immune-related genes from G. bimaculatus indicates the existence of a sophisticated and specialized broad spectrum immune mechanism against invading pathogens, which provides, for the first time, insights into the molecular mechanism of disease resistance among two-spotted field crickets.

scholarly journals De novo transcriptome assembly of Premnotrypes vorax (Coleoptera: Curculionidae)

2020 ◽  
Author(s):  
Luisa-Fernanda Velásquez C. ◽  
Pablo Emiliano Canton ◽  
Alejandro Sánchez-Flores ◽  
Alejandra Bravo ◽  
Jairo Cerón
Keyword(s):  
Biological Control ◽  
Control Strategy ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Insect Pest ◽  
Illumina Hiseq ◽  
Tissue Samples ◽  
Cry Toxin ◽  
Illumina Hiseq Platform ◽  
Potato Crops

Abstract Objective: Premnotrypes vorax (P. vorax) is an insect pest that causes significant losses to potato crops in Colombia. Currently, the insect control is mainly done by using highly toxic chemical insecticides and there are no reports of any commercial biological control strategy against this pest. Hence, the objective of this study was to characterize the insect genetic expression to search for genes that could codify for Bacillus thuringiensis Cry toxin receptors. Using an RNA-seq approach, we sequenced the mRNA from the insect tissue, performed a de novo assembly and analyzed the reconstructed transcriptome of P. vorax. To our knowledge, this is the first genetic report of this endemic insect which will set the basis of a possible biological control strategy.Results: The transcriptome data was obtained from dissected midgut tissue samples of P. vorax larvae. The isolated RNA was isolated and sequenced using the Illumina HiSeq platform with a configuration of 2x150pb reads. A total of 383,552,246 reads were obtained and subsequently a quality and cleaning process was performed through FastQC and Trimmomatic software, respectively. A novo assembly was done using the Trinity software, obtaining a transcriptome assembly with 25,631 genes that showed at least one annotation record, resulting in 74,984 transcript isoforms.

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