scholarly journals Comparative RNA-Seq analysis reveals genes associated with masculinization in female Cannabis sativa

Planta ◽  
2021 ◽  
Vol 253 (1) ◽  
Author(s):  
Ayelign M. Adal ◽  
Ketan Doshi ◽  
Larry Holbrook ◽  
Soheil S. Mahmoud
Keyword(s):  
Differentially Expressed Genes ◽  
Cannabis Sativa ◽  
Expression Patterns ◽  
Plant Biotechnology ◽  
Male Flower ◽  
Sex Expression ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Rna Profiling ◽  
Male Flowers

Abstract Main conclusion Using RNA profiling, we identified several silver thiosulfate-induced genes that potentially control the masculinization of female Cannabis sativa plants. Abstract Genetically female Cannabis sativa plants normally bear female flowers, but can develop male flowers in response to environmental and developmental cues. In an attempt to elucidate the molecular elements responsible for sex expression in C. sativa plants, we developed genetically female lines producing both female and chemically-induced male flowers. Furthermore, we carried out RNA-Seq assays aimed at identifying differentially expressed genes responsible for male flower development in female plants. The results revealed over 10,500 differentially expressed genes, of which around 200 potentially control masculinization of female cannabis plants. These genes include transcription factors and other genes involved in male organ (i.e., anther and pollen) development, as well as genes involved in phytohormone signalling and male-biased phenotypes. The expressions of 15 of these genes were further validated by qPCR assay confirming similar expression patterns to that of RNA-Seq data. These genes would be useful for understanding predisposed plants producing flowers of both sex types in the same plant, and help breeders to regulate the masculinization of female plants through targeted breeding and plant biotechnology.

scholarly journals Genome-Wide Expression Profiles of Hemp (Cannabis sativa L.) in Response to Drought Stress

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Chunsheng Gao ◽  
Chaohua Cheng ◽  
Lining Zhao ◽  
Yongting Yu ◽  
Qing Tang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Differentially Expressed Genes ◽  
Cannabis Sativa ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Signal Transduction Pathway ◽  
Differentially Expressed ◽  
Growth And Yield ◽  
Rna Seq ◽  
Kegg Pathways

Drought is the main environmental factor impairing hemp growth and yield. In order to decipher the molecular responses of hemp to drought stress, transcriptome changes of drought-stressed hemp (DS1 and DS2), compared to well-watered control hemp (CK1 and CK2), were studied with RNA-Seq technology. RNA-Seq generated 9.83, 11.30, 11.66, and 11.31 M clean reads in the CK1, CK2, DS1, and DS2 libraries, respectively. A total of 1292 differentially expressed genes (DEGs), including 409 (31.66%) upregulated and 883 (68.34%) downregulated genes, were identified. The expression patterns of 12 selected genes were validated by qRT-PCR, and the results were accordant with Illumina analysis. Gene Ontology (GO) and KEGG analysis illuminated particular important biological processes and pathways, which enriched many candidate genes such as NAC, B3, peroxidase, expansin, and inositol oxygenase that may play important roles in hemp tolerance to drought. Eleven KEGG pathways were significantly influenced, the most influenced being the plant hormone signal transduction pathway with 15 differentially expressed genes. A similar expression pattern of genes involved in the abscisic acid (ABA) pathway under drought, and ABA induction, suggested that ABA is important in the drought stress response of hemp. These findings provide useful insights into the drought stress regulatory mechanism in hemp.

scholarly journals Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain

2019 ◽  
Author(s):  
Ailing Liu ◽  
Zhibo Zhou ◽  
Yake Yi ◽  
Guanghui Chen
Keyword(s):  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Critical Role ◽  
Differentially Expressed ◽  
Rice Grain ◽  
Rna Seq ◽  
Cd Stress ◽  
Cd Accumulation ◽  
Cadmium Transport ◽  
Central Organ

Abstract Background: Node is the central organ of xylem to phloem transfer of nutrients and ions in plants. Cadmium (Cd)-induced crop pollution threatens food safety. Breeding cultivar with low Cd accumulation is a chance to resolve this universal problem. This study was performed to identify tissue specific genes involved in Cd accumulation in different rice stem nodes. Panicle node and the first node under panicle (node I) were sampled in two rice cultivars: Xiangwanxian No. 12 with low Cd accumulation and Yuzhenxiang with high Cd accumulation in the grains. RNA-seq analysis was performed to identify differentially expressed genes (DEGs) and microRNAs. Results: Xiangwanxian No. 12 had lower Cd concentration in panicle node, node I and grain compared with Yuzhenxiang , and node Ⅰ had the highest Cd concentration in the two cultivars. RNA seq analysis identified 4,535 differentially expressed genes and 70 miRNAs between the two cultivars. Most genes ( OsIRT1 , OsNramp5, OsVIT2 , OsNRT1.5A, and OsABCC1 ) related to the “transporter activity” blocked the transport of Cd up to panicle and accumulation in grains of low Cd-accumulative cultivar. Among the genes related to “response to stimulus”, we identified OsHSP70 and OsHSFA2d/B2c in “X”, but not in “y”, were all down-regulated by Cd stimulus. The up-regulation of miRNAs ( osa-miR528 and osa-miR408 ) played a potent role in lowering Cd accumulation via down regulation of genes, such as bZIP , ERF , MYB , SnRK1 and HSPs in Xiangwanxian No. 12 cultivar. Conclusions: Both panicle node and node I of Xiangwanxian No. 12 played a key role in blocking the upward transportation of Cd, while node I played a critical role in Yuzhenxiang . Distinct expression patterns of various transporter genes such as OsNRT1.5A, OsNramp5, OsIRT1, OsVIT2 and OsABCC1 resulted in differential Cd accumulation in different nodes. Likewise, distinct expression patterns of these transporter genes are likely responsible for the low Cd accumulation in Xiangwanxian No. 12 cultivar . MiRNAs drove multiple transcription factors, such as OsbZIPs, OsERFs, OsMYBs , to play a role in stress response, which contribute to the response to Cd stress in rice.

scholarly journals Transcriptomic analysis reveals distinct resistant response by physcion and chrysophanol against cucumber powdery mildew

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1991 ◽  
Author(s):  
Yanping Li ◽  
Shilin Tian ◽  
Xiaojun Yang ◽  
Xin Wang ◽  
Yuhai Guo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Disease Resistance ◽  
Powdery Mildew ◽  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Defense Responses ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Sequencing Data ◽  
Transcriptional Change

Physcion and chrysophanol induce defense responses against powdery mildew in cucumbers. The combination of these two compounds has synergistic interaction against the disease. We performed RNA-seq on cucumber leaf samples treated with physcion and chrysophanol alone and with their combination. We generated 17.6 Gb of high-quality sequencing data (∼2 Gb per sample) and catalogued the expressions profiles of 12,293 annotated cucumber genes in each sample. We identified numerous differentially expressed genes that exhibited distinct expression patterns among the three treatments. The gene expression patterns of the Chr and Phy treatments were more similar to each other than to the Phy × Chr treatment. The Phy × Chr treatment induced the highest number of differentially expressed genes. This dramatic transcriptional change after Phy × Chr treatment leaves reflects that physcion combined with chrysophanol treatment was most closely associated with induction of disease resistance. The analysis showed that the combination treatment caused expression changes of numerous defense-related genes. These genes have known or potential roles in structural, chemical and signaling defense responses and were enriched in functional gene categories potentially responsible for cucumber resistance. These results clearly demonstrated that disease resistance in cucumber leaves was significantly influenced by the combined physcion and chrysophanol treatment. Thus, physcion and chrysophanol are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to the defense response.

scholarly journals Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain

2019 ◽  
Author(s):  
Ailing Liu ◽  
Zhibo Zhou ◽  
Yake Yi ◽  
Guanghui Chen
Keyword(s):  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Critical Role ◽  
Differentially Expressed ◽  
Rice Grain ◽  
Rna Seq ◽  
Cd Accumulation ◽  
Cadmium Transport ◽  
Upward Transport ◽  
Central Organ

Abstract Background: Node is the central organ of xylem to phloem transfer of nutrients and ions in plants. Cadmium (Cd)-induced crop pollution threatens food safety. Breeding cultivar with low Cd accumulation is a chance to resolve this universal problem. This study was performed to identify tissue specific genes involved in Cd accumulation in different rice stem nodes. Panicle node and the first node under panicle (node I) were sampled in two rice cultivars: Xiangwanxian No. 12 with low Cd accumulation and Yuzhenxiang with high Cd accumulation in the grains. RNA-seq analysis was performed to identify differentially expressed genes (DEGs) and microRNAs. Results: Xiangwanxian No. 12 had lower Cd concentration in panicle node, node I and grain compared with Yuzhenxiang, and node Ⅰ had the highest Cd concentration in the two cultivars. RNA seq analysis identified 4,535 differentially expressed genes and 70 miRNAs between the two cultivars. Most genes (OsIRT1, OsNramp5, OsVIT2, OsNRT1.5A, and OsABCC1) related to the “transporter activity” play roles in blocking the upward transport of Cd in the low Cd-accumulative cultivar. Among the genes related to “response to stimulus”, we identified OsHSP70 and OsHSFA2d/B2c in Xiangwanxian No. 12, but not in Yuzhenxiang, were all down-regulated by Cd stimulus. The up-regulation of miRNAs (osa-miR528 and osa-miR408) played a potent role in lowering Cd accumulation via down regulation of genes, such as bZIP, ERF, MYB, SnRK1 and HSPs in Xiangwanxian No. 12 cultivar. Conclusions: Both panicle node and node I of Xiangwanxian No. 12 played a key role in blocking the upward transportation of Cd, while node I played a critical role in Yuzhenxiang. Distinct expression patterns of various transporter genes such as OsNRT1.5A, OsNramp5, OsIRT1, OsVIT2 and OsABCC1 resulted in differential Cd accumulation in different nodes. Likewise, distinct expression patterns of these transporter genes are likely responsible for the low Cd accumulation in Xiangwanxian No. 12 cultivar. MiRNAs drove multiple transcription factors, such as OsbZIPs, OsERFs, OsMYBs, to play a role in stress response, which contribute to the response to Cd stress in rice.

scholarly journals In Silico Analysis and Characterization of Differentially Expressed Genes to Distinguish Glioma Stem Cells from Normal Neural Stem Cells

2021 ◽  
Author(s):  
Urja Parekh ◽  
Mohit Mazumder ◽  
Harpreet Kaur ◽  
Elia Brodsky
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Neural Stem Cells ◽  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Principal Component ◽  
Differentially Expressed ◽  
Glioma Stem Cells ◽  
Rna Seq ◽  
Bioinformatics Analyses

AbstractGlioblastoma multiforme (GBM) is a heterogeneous, invasive primary brain tumor that develops chemoresistance post therapy. Theories regarding the aetiology of GBM focus on transformation of normal neural stem cells (NSCs) to a cancerous phenotype or tumorigenesis driven via glioma stem cells (GSCs). Comparative RNA-Seq analysis of GSCs and NSCs can provide a better understanding of the origin of GBM. Thus, in the current study, we performed various bioinformatics analyses on transcriptional profiles of a total 40 RNA-seq samples including 20 NSC and 20 GSC, that were obtained from the NCBI-SRA (SRP200400). First, differential gene expression (DGE) analysis using DESeq2 revealed 358 significantly differentially expressed genes between GSCs and NSCs (padj. value <0.05, log2fold change ±3) with 192 upregulated and 156 downregulated genes in GSCs in comparison to NSCs. Subsequently, exploratory data analysis using the principal component analysis (PCA) based on key significant genes depicted the clear separation between both the groups. Further, the Hierarchical clustering confirmed the distinct clusters of GSC and NSC samples. Eventually, the biological enrichment analysis of the significant genes showed their enrichment in tumorigenesis pathways such as Wnt-signalling, VEGF- signalling and TGF-β-signalling pathways. Conclusively, our study depicted significant differences in the gene expression patterns between NSCs and GSCs. Besides, we also identified novel genes and genes previously unassociated with gliomagenesis that may prove to be valuable in establishing diagnostic, prognostic biomarkers and therapeutic targets for GBM.

scholarly journals Transcriptome Analysis Reveals Skin Lipid Metabolism Related to Wool Diameter in Sheep

2016 ◽  
Author(s):  
Shaoyin Fu ◽  
YunXia Qi ◽  
Xiaolong He ◽  
Lai Da ◽  
biao Wang ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Differentially Expressed Genes ◽  
Fiber Diameter ◽  
Expression Patterns ◽  
Wool Fiber ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Skin Lipid ◽  
Skin Development ◽  
Qrt Pcr

AbstractWool is one of the most important animal fibers in the textile industry and the diameter directly affects its economic value. However, the molecular mechanisms underlying the wool diameter have not been fully elucidated. In the present study, high-throughput RNA-Seq technology was employed to explore the skin transcriptome using 3 sheep with fine wool (fiber diameter, FD<21.0μm) and 3 sheep with coarse wool (fiber diameter, FD>27.0μm). In total, 28,607,228 bp clean reads were obtained, and 78.88%+/-3.84% was uniquely aligned to the reference genome across the six samples. In total, 19,914 mRNA transcripts were expressed (FPKM>0) in the six skin samples, among which there were certain well-known genes affecting the skin hair cycle, such as KRTAP7-1, KRT14, Wnt10b, Wnt2b, β-catenin, and FGF5. Furthermore, 467 expressed genes were significantly differentially expressed between the two groups, including 21 genes up-regulated and 446 genes down-regulated in the sheep with the smaller fiber diameter. To verify the results, 13 differentially expressed genes were randomly selected to validate the expression patterns using qRT-PCR, and the correlation between the mRNA expression level from qRT-PCR and RNA-Seq data was 0.999 ( P<0.05). These differentially expressed genes were particularly enriched in GO processes related to lipid metabolism, skin development, differentiation, and immune function (P<0.05). The biological processes were involved in collagen catabolism, negative regulation of macromolecule metabolism, steroid hormone stimulation and lipid metabolism. A significant KEGG pathway involving the “metabolism of lipids and lipoproteins” was also enriched. This study revealed that the lipid metabolism might constitute one of the major factors related to wool diameter.

RNA-Seq Transcriptome Profiling Reveals Differentially Expressed Genes Involved in Sex Expression in Melon

Crop Science ◽  
2015 ◽  
Vol 55 (4) ◽  
pp. 1686-1695 ◽  
Author(s):  
Peng Gao ◽  
Yunyan Sheng ◽  
Feishi Luan ◽  
Hongyan Ma ◽  
Shi Liu
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Profiling ◽  
Sex Expression ◽  
Differentially Expressed ◽  
Rna Seq

scholarly journals A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Aliki Xanthopoulou ◽  
Javier Montero-Pau ◽  
Belén Picó ◽  
Panagiotis Boumpas ◽  
Eleni Tsaliki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cucurbita Pepo ◽  
Developmental Stages ◽  
Lateral Roots ◽  
Expression Patterns ◽  
Male Flower ◽  
Differentially Expressed ◽  
Gene Expression Atlas ◽  
Summer Squash ◽  
Expression Atlas

Abstract Background Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Results In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,000 genes common to all tissue groups. Of these, 3812 were identified as housekeeping genes, half of which assigned to known gene ontologies. Flowers, seeds, and young fruits had the largest number of specific genes, whilst intermediate-age fruits the fewest. There also were genes that were differentially expressed in the various tissues, the male flower being the tissue with the most differentially expressed genes in pair-wise comparisons with the remaining tissues, and the leaf stem the least. The largest expression change during fruit development was early on, from female flower to fruit two days after pollination. A weighted correlation network analysis performed on the global gene expression dataset assigned 25,413 genes to 24 coexpression groups, and some of these groups exhibited strong tissue specificity. Conclusions These findings enrich our understanding about the transcriptomic events associated with summer squash development and ripening. This comprehensive gene expression atlas is expected not only to provide a global view of gene expression patterns in all major tissues in C. pepo but to also serve as a valuable resource for functional genomics and gene discovery in Cucurbitaceae.

scholarly journals Transcriptome Expression of Biomineralization Genes in Littoraria flava Gastropod in Brazilian Rocky Shore Reveals Evidence of Local Adaptation

2021 ◽  
Vol 13 (4) ◽  
Author(s):  
Camilla A Santos ◽  
Gabriel G Sonoda ◽  
Thainá Cortez ◽  
Luiz L Coutinho ◽  
Sónia C S Andrade
Keyword(s):  
Local Adaptation ◽  
Differentially Expressed Genes ◽  
Evolutionary Biology ◽  
Rocky Shore ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Marine Species ◽  
Differentially Expressed ◽  
Planktonic Larva ◽  
Structure Changes

Abstract Understanding how selection shapes population differentiation and local adaptation in marine species remains one of the greatest challenges in the field of evolutionary biology. The selection of genes in response to environment-specific factors and microenvironmental variation often results in chaotic genetic patchiness, which is commonly observed in rocky shore organisms. To identify these genes, the expression profile of the marine gastropod Littoraria flava collected from four Southeast Brazilian locations in ten rocky shore sites was analyzed. In this first L. flava transcriptome, 250,641 unigenes were generated, and 24% returned hits after functional annotation. Independent paired comparisons between 1) transects, 2) sites within transects, and 3) sites from different transects were performed for differential expression, detecting 8,622 unique differentially expressed genes. Araçá (AR) and São João (SJ) transect comparisons showed the most divergent gene products. For local adaptation, fitness-related differentially expressed genes were chosen for selection tests. Nine and 24 genes under adaptative and purifying selection, respectively, were most related to biomineralization in AR and chaperones in SJ. The biomineralization-genes perlucin and gigasin-6 were positively selected exclusively in the site toward the open ocean in AR, with sequence variants leading to pronounced protein structure changes. Despite an intense gene flow among L. flava populations due to its planktonic larva, gene expression patterns within transects may be the result of selective pressures. Our findings represent the first step in understanding how microenvironmental genetic variation is maintained in rocky shore populations and the mechanisms underlying local adaptation in marine species.

Sign in / Sign up

Export Citation Format

Share Document