scholarly journals Metabolome and Transcriptome Analysis Reveals Putative Genes Involved in Anthocyanin Accumulation and Coloration in White and Pink Tea (Camellia sinensis) Flower

Molecules ◽  
2020 ◽  
Vol 25 (1) ◽  
pp. 190 ◽  
Author(s):  
Caibi Zhou ◽  
Xin Mei ◽  
Dylan O’Neill Rothenberg ◽  
Zaibo Yang ◽  
Wenting Zhang ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Syringic Acid ◽  
Anthocyanin Accumulation ◽  
Rna Seq ◽  
Tea Tree ◽  
Insight Into

A variant of tea tree (Camellia sinensis (L.)) with purple buds and leaves and pink flowers can be used as a unique ornamental plant. However, the mechanism of flower coloration remains unclear. To elucidate the molecular mechanism of coloration, as well as anthocyanin accumulation in white and pink tea flowers, metabolite profiling and transcriptome sequencing was analyzed in various tea flower developmental stages. Results of metabolomics analysis revealed that three specific anthocyanin substances could be identified, i.e., cyanidin O-syringic acid, petunidin 3-O-glucoside, and pelargonidin 3-O-β-d-glucoside, which only accumulated in pink tea flowers, and were not able to be detected in white flowers. RNA-seq and weighted gene co-expression network analysis revealed eight highly expressed structural genes involved in anthocyanin biosynthetic pathway, and particularly, different expression patterns of flavonol synthase and dihydroflavonol-4-reductase genes were observed. We deduced that the disequilibrium of expression levels in flavonol synthases and dihydroflavonol-4-reductases resulted in different levels of anthocyanin accumulation and coloration in white and pink tea flowers. Results of qRT-PCR performed for 9 key genes suggested that the expression profiles of differentially expressed genes were generally consistent with the results of high-throughput sequencing. These findings provide insight into anthocyanin accumulation and coloration mechanisms during tea flower development, which will contribute to the breeding of pink-flowered and anthocyanin-rich tea cultivars.

scholarly journals MicroRNA-1 Expression and Function in Hyalomma Anatolicum anatolicum (Acari: Ixodidae) Ticks

2021 ◽  
Vol 12 ◽  
Author(s):  
Jin Luo ◽  
Qiaoyun Ren ◽  
Wenge Liu ◽  
Xiaofei Qiu ◽  
Gaofeng Zhang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Gene Selection ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Tissue Expression ◽  
Hyalomma Anatolicum ◽  
Internal Reference ◽  
Hyalomma Anatolicum Anatolicum ◽  
Significant Difference

MicroRNAs act as mRNA post-transcriptional regulators, playing important roles in cell differentiation, transcriptional regulation, growth, and development. In this study, microRNA expression profiles of Hyalomma anatolicum anatolicum ticks at different developmental stages were detected by high-throughput sequencing and functionally assessed. In total, 2,585,169, 1,252,678, 1,558,217, and 1,155,283 unique reads were obtained from eggs, larvae, nymphs, and adults, respectively, with 42, 46, 45, and 41 conserved microRNAs in these stages, respectively. Using eggs as a control, 48, 43, and 39 microRNAs were upregulated, and 3, 10, and 9 were downregulated in larvae, nymphs, and adults, respectively. MicroRNA-1 (miR-1) was expressed in high abundance throughout Ha. anatolicum development, with an average of nearly one million transcripts, and it is highly conserved among tick species. Quantitative real-time PCR (qPCR) showed that miR-1 expression gradually increased with tick development, reaching the highest level at engorgement. Differential tissue expression was detected, with significantly higher levels in the salivary glands and epidermis than in the midgut. Inhibition assays showed no significant change in body weight or spawning time or amount between experimental and control groups, but there was a significant difference (p < 0.01) in engorgement time. With miR-1 inhibition, ticks displayed obvious deformities during later development. To more fully explain the microRNA mechanism of action, the miR-1 cluster was analyzed according to the target gene; members that jointly act on Hsp60 include miR-5, miR-994, miR-969, and miR-1011. Therefore, microRNAs are critical for normal tick development, and the primary structure of the mature sequence of miR-1 is highly conserved. Nonetheless, different developmental stages and tissues show different expression patterns, with a certain role in prolonging feeding. miR-1, together with other cluster members, regulates mRNA function and may be used as a molecular marker for species origin, evolution analysis, and internal reference gene selection.

scholarly journals Integrated analysis of the metabolome and transcriptome in different developmental stages of Cerasus humilis peel coloration

2020 ◽  
Author(s):  
Xiaolong Ji ◽  
Jing Ren ◽  
Lijiao Sun ◽  
Shaoyu Lang ◽  
Liwei Zhu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Syringic Acid ◽  
Integrated Analysis ◽  
Fruit Peel ◽  
Qrt Pcr ◽  
Cerasus Humilis ◽  
Important Trait ◽  
Insight Into ◽  
Anthocyanin Biosynthetic Genes

Abstract Background: Cerasus humilis is a unique dwarf shrub and fruit color is an important trait in the species. In this study, we evaluated the transcriptomic and metabolomic profiles of the plant at different developmental stages to elucidate the mechanism underlying color formation.Results: In a metabolomics analysis, 16 anthocyanin components were identified at different developmental stages, and high levels of cyanidin O-syringic acid and pelargonidin 3-O-beta-d-glucoside (callistephin chloride) were correlated with the reddening of the fruit peel. Additionally, transcriptome analysis showed that most anthocyanin biosynthetic genes and two MYB transcription factors were significantly up-regulated. qRT-PCR results for these differentially expressed genes were generally consistent with the high-throughput sequencing. A co-expression analysis revealed that ANS and UFGT play keys role in pigmentation. Conclusions: These findings provide insight into the mechanisms underlying anthocyanin accumulation and coloration during fruit peel development, providing a basis for the breeding of anthocyanin-rich C. humilis cultivars.

scholarly journals RNA-Seq analysis of genes affected by Cyclophilin A/DIAGEOTROPICA (DGT) in tomato root development

2020 ◽  
Author(s):  
Maria G. Ivanchenko ◽  
Olivia R. Ozguc ◽  
Stephanie R. Bollmann ◽  
Valerie N. Fraser ◽  
Molly Megraw
Keyword(s):  
Developmental Stages ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cyclophilin A ◽  
Developmental Pathways ◽  
Root Tip ◽  
Rna Seq ◽  
Tomato Root ◽  
Initial Comparison ◽  
Insight Into

AbstractCyclophilin A/DIAGEOTROPICA (DGT) has been linked to auxin-regulated development in tomato and appears to affect multiple developmental pathways. Loss of DGT function results in a pleiotropic phenotype that is strongest in the roots, including shortened roots with no lateral branching. Here, we present an RNA-Seq dataset comparing the gene expression profiles of wildtype (‘Ailsa Craig’) and dgt tissues from three spatially separated developmental stages of the tomato root tip, with three replicates for each tissue and genotype. We also identify differentially expressed genes, provide an initial comparison of genes affected in each genotype and tissue, and provide the pipeline used to analyze the data. Further analysis of this dataset can be used to gain insight into the effects of DGT on various root developmental pathways in tomato.

scholarly journals Integrated Analysis of the Metabolome and Transcriptome on Anthocyanin Biosynthesis in Four Developmental Stages of Cerasus humilis Peel Coloration

2021 ◽  
Vol 22 (21) ◽  
pp. 11880
Author(s):  
Xiaolong Ji ◽  
Jing Ren ◽  
Yixin Zhang ◽  
Shaoyu Lang ◽  
Di Wang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Syringic Acid ◽  
Integrated Analysis ◽  
Fruit Peel ◽  
Cerasus Humilis ◽  
Important Trait ◽  
Anthocyanin Biosynthetic Genes

Cerasus humilis is a unique dwarf shrub and fruit color is an important trait in the species. In this study, we evaluated the transcriptomic and metabolomic profiles of the plant at different developmental stages to elucidate the mechanism underlying color formation. In a metabolomics analysis, 16 anthocyanin components were identified at four developmental stages, and high levels of cyanidin O-syringic acid and pelargonidin 3-O-beta-d-glucoside (callitephin chloride) were correlated with the reddening of the fruit peel. A co-expression analysis revealed that ANS and UFGT play key roles in pigmentation (PCC > 0.82). Additionally, transcriptome data showed that most anthocyanin biosynthetic genes and two MYB transcription factors were significantly up-regulated. QRT-PCR results for these differentially expressed genes were generally consistent with the high-throughput sequencing. Moreover, the overexpression of ChMYB1 (TRINITY_DN21536_c0_g1) in apple calli could contribute to the accumulation of anthocyanin. It was also found that UFGT (TRINITY_DN19893_c1_g5) and ChMYB1 (TRINITY_DN21536_c0_g1) have similar expression patterns. These findings provide insight into the mechanisms underlying anthocyanin accumulation and coloration during fruit peel development, providing a basis for the breeding of anthocyanin-rich C. humilis cultivars.

scholarly journals Structural and functional insights into the LBD family involved in abiotic stress and flavonoid synthases in Camellia sinensis

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Xueying Zhang ◽  
Yuqing He ◽  
Wenda He ◽  
Hui Su ◽  
Yuefei Wang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Camellia Sinensis ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Flavonoid Biosynthesis ◽  
Gene Promoters ◽  
Rna Seq ◽  
Lateral Organ ◽  
Insight Into

Abstract Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors that play a crucial role in growth and development, as well as metabolic processes. However, knowledge of the function of LBD proteins in Camellia sinensis is limited, and no systematic investigations of the LBD family have been reported. In this study, we identified 54 LBD genes in Camellia sinensis. The expression patterns of CsLBDs in different tissues and their transcription responses to exogenous hormones and abiotic stress were determined by RNA-seq, which showed that CsLBDs may have diverse functions. Analysis of the structural gene promoters revealed that the promoters of CsC4H, CsDFR and CsUGT84A, the structural genes involved in flavonoid biosynthesis, contained LBD recognition binding sites. The integrative analysis of CsLBD expression levels and metabolite accumulation also suggested that CsLBDs are involved in the regulation of flavonoid synthesis. Among them, CsLOB_3, CsLBD36_2 and CsLBD41_2, localized in the nucleus, were selected for functional characterization. Yeast two-hybrid assays revealed that CsLBD36_2 and CsLBD41_2 have self-activation activities, and CsLOB_3 and CsLBD36_2 can directly bind to the cis-element and significantly increase the activity of the CsC4H, CsDFR and CsUGT84A promoter. Our results present a comprehensive characterization of the 54 CsLBDs in Camellia sinensis and provide new insight into the important role that CsLBDs play in abiotic and flavonoid biosynthesis.

scholarly journals RNA-Seq analysis of genes affected by Cyclophilin A/DIAGEOTROPICA (DGT) in tomato root development

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1175
Author(s):  
Maria G. Ivanchenko ◽  
Olivia R. Ozguc ◽  
Stephanie R. Bollmann ◽  
Valerie N. Fraser ◽  
Molly Megraw
Keyword(s):  
Developmental Stages ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cyclophilin A ◽  
Developmental Pathways ◽  
Root Tip ◽  
Rna Seq ◽  
Tomato Root ◽  
Initial Comparison ◽  
Insight Into

Cyclophilin A/DIAGEOTROPICA (DGT) has been linked to auxin-regulated development in tomato and appears to affect multiple developmental pathways. Loss of DGT function results in a pleiotropic phenotype that is strongest in the roots, including shortened roots with no lateral branching. Here, we present an RNA-Seq dataset comparing the gene expression profiles of wildtype (‘Ailsa Craig’) and dgt tissues from three spatially separated developmental stages of the tomato root tip, with three replicates for each tissue and genotype. We also identify differentially expressed genes, provide an initial comparison of genes affected in each genotype and tissue, and provide the pipeline used to analyze the data. Further analysis of this dataset can be used to gain insight into the effects of DGT on various root developmental pathways in tomato.

scholarly journals Genomic and Transcriptomic Analysis Reveals Cuticular Protein Genes Responding to Different Insecticides in Fall Armyworm Spodoptera frugiperda

Insects ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 997
Author(s):  
Jia-Ying Zhu ◽  
Lu Li ◽  
Kai-Ran Xiao ◽  
Shu-Qi He ◽  
Fu-Rong Gui
Keyword(s):  
Spodoptera Frugiperda ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Fall Armyworm ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Specific Expression ◽  
Functional Investigation

The fall armyworm (FAW), Spodoptera frugiperda, is a serious pest of crucial crops causing great threats to the food security of the world. It has evolved resistance to various insecticides, while the underlying molecular mechanisms remain largely unknown. Cuticular proteins (CPs), as primary components in cuticle, play an important role in insects’ protection against environmental stresses. Few of them have been documented as participating in insecticide resistance in several insect species. In order to explore whether CP genes of the FAW exhibit a functional role in responding to insecticides stress, a total of 206 CPs, classified into eight families, were identified from the genome of the FAW through a homology-based approach coupled with manual efforts. The temporal expression profiles of all identified CP genes across developmental stages and their responses to 23 different insecticides were analyzed using the RNA-seq data. Expression profiling indicated that most of the CP genes displayed stage-specific expression patterns. It was found that the expression of 51 CP genes significantly changed after 48 h exposure to 17 different insecticides. The expression of eight CP genes responding to four insecticides were confirmed by RT-PCR analysis. The results showed that their overall expression profiles were consistent with RNA-seq analysis. The findings provide a basis for further functional investigation of CPs implied in insecticide stress in FAW.

scholarly journals MicroRNA-1 promotes the development of and prolongs engorgement time in Hyalomma anatolicum anatolicum (Acari: Ixodidae) ticks

2020 ◽  
Author(s):  
Jin Luo ◽  
Qiaoyun Ren ◽  
Wenge Liu ◽  
Xiaofei Qiu ◽  
Gaofeng Zhang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Gene Selection ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Hyalomma Anatolicum ◽  
Internal Reference ◽  
Hyalomma Anatolicum Anatolicum ◽  
Origin And Evolution ◽  
Significant Difference

AbstractMicroRNAs act as mRNA posttranscriptional regulators, playing important roles in cell differentiation, transcriptional regulation, growth and development. In this study, microRNA expression profiles of Hyalomma anatolicum anatolicum ticks at different developmental stages were detected by high-throughput sequencing and functionally assessed. In total, 2,585,169, 1,252,678, 1,558,217 and 1,155,283 unique reads were obtained from eggs, larvae, nymphs and adults, respectively, with 42, 46, 45 and 41 conserved microRNAs in these stages, respectively. Using eggs as a control, 48, 43 and 39 microRNAs were upregulated and 3, 10 and 9 downregulated in larvae, nymphs and adults, respectively. microRNA-1 (miR-1) was expressed in high abundance throughout Ha. anatolicum development, with an average of nearly one million transcripts, and it is highly conserved among tick species. Quantitative real-time PCR (qPCR) showed that miR-1 expression gradually increased with tick development, reaching the highest level at engorgement. Differential tissue expression was detected, with significantly higher levels in the salivary glands and epidermis than in the midgut. Inhibition assays showed no significant change in body weight or spawning time or amount between experimental and control groups, but there was a significant difference (p<0.01) in engorgement time. With miR-1 inhibition, ticks displayed obvious deformities during later development. To more fully explain the microRNA mechanism of action, the miR-1 family was analyzed regarding target gene; members acting on Hsp60 include miR-5, miR-994, miR-969, and miR-1011, which jointly play a role. Therefore, microRNAs are critical for normal tick development, and the primary structure of the mature sequence of miR-1 is highly conserved. Nonetheless, different developmental stages and tissues show different expression patterns, with a certain role in prolonging feeding. miR-1, together with other family members, regulates mRNA function and may be used as a molecular marker for species origin and evolution analysis and internal reference gene selection.

scholarly journals Transcriptome and Metabolome Analyses of the Flowers and Leaves of Chrysanthemum dichrum

2021 ◽  
Vol 12 ◽  
Author(s):  
Hua Liu ◽  
Xiaoxi Chen ◽  
Hạixia Chen ◽  
Jie Lu ◽  
Dongliang Chen ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Average Length ◽  
Expression Patterns ◽  
Rna Seq ◽  
Flower Buds ◽  
The Family ◽  
Polymerase Chain ◽  
Chrysanthemum Dichrum

Chrysanthemum dichrum is an important wild species in the family Asteraceae. However, because of a lack of genetic information, there has been relatively little research conducted on the molecular mechanisms in C. dichrum. There is no report describing the transcriptome and metabolome of C. dichrum flowers and leaves at different developmental stages. In this study, high-throughput sequencing and RNA-seq analyses were used to investigate the transcriptome of C. dichrum leaves, flower buds, and blooming flowers. Additionally, these three tissues also underwent a metabolomics analysis. A total of 447,313,764 clean reads were assembled into 77,683 unigenes, with an average length of 839 bp. Of the 44,204 annotated unigenes, 42,189, 28,531, 23,420, and 17,599 were annotated using the Nr, Swiss-Prot, KOG, and KEGG databases, respectively. Furthermore, 31,848 differentially expressed genes (DEGs) were detected between the leaves and flower buds, whereas 23,197 DEGs were detected between the leaves and blooming flowers, and 11,240 DEGs were detected between the flower buds and blooming flowers. Finally, a quantitative real-time Polymerase Chain Reaction (qRT-PCR) assay was conducted to validate the identified DEGs. The metabolome data revealed several abundant metabolites in C. dichrum leaves, flower buds, and blooming flowers, including raffinose, 1-kestose, asparagine, glutamine, and other medicinal compounds. The expression patterns of significant DEGs revealed by the transcriptome analysis as well as the data for the differentially abundant metabolites in three C. dichrum tissues provide important genetic and metabolic information relevant for future investigations of the molecular mechanisms in C. dichrum. Moreover, the results of this study may be useful for the molecular breeding, development, and application of C. dichrum resources.

scholarly journals Genome-Wide Analysis and Characterization of the Aux/IAA Family Genes Related to Floral Scent Formation in Hedychium coronarium

2019 ◽  
Vol 20 (13) ◽  
pp. 3235 ◽  
Author(s):  
Yanguo Ke ◽  
Farhat Abbas ◽  
Yiwei Zhou ◽  
Rangcai Yu ◽  
Yuechong Yue ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Floral Scent ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Cut Flowers ◽  
Flower Opening ◽  
Hedychium Coronarium

Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.

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