scholarly journals Capsicum chinense MYB Transcription Factor Genes: Identification, Expression Analysis, and Their Conservation and Diversification With Other Solanaceae Genomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Khushbu Islam ◽  
Abdul Rawoof ◽  
Ilyas Ahmad ◽  
Meenakshi Dubey ◽  
John Momo ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Expression Patterns ◽  
Fruit Shape ◽  
Myb Transcription Factor ◽  
Pcr Analysis ◽  
Transcriptome Data ◽  
Capsicum Chinense ◽  
Significant Differential Expression ◽  
Qrt Pcr ◽  
Capsaicinoid Biosynthesis

Myeloblastosis (MYB) genes are important transcriptional regulators of plant growth, development, and secondary metabolic biosynthesis pathways, such as capsaicinoid biosynthesis in Capsicum. Although MYB genes have been identified in Capsicum annuum, no comprehensive study has been conducted on other Capsicum species. We identified a total of 251 and 240 MYB encoding genes in Capsicum chinense MYBs (CcMYBs) and Capsicum baccatum MYBs (CbMYBs). The observation of twenty tandem and 41 segmental duplication events indicated expansion of the MYB gene family in the C. chinense genome. Five CcMYB genes, i.e., CcMYB101, CcMYB46, CcMYB6, CcPHR8, and CcRVE5, and two CaMYBs, i.e., CaMYB3 and CaHHO1, were found within the previously reported capsaicinoid biosynthesis quantitative trait loci. Based on phylogenetic analysis with tomato MYB proteins, the Capsicum MYBs were classified into 24 subgroups supported by conserved amino acid motifs and gene structures. Also, a total of 241 CcMYBs were homologous with 225 C. annuum, 213 C. baccatum, 125 potato, 79 tomato, and 23 Arabidopsis MYBs. Synteny analysis showed that all 251 CcMYBs were collinear with C. annuum, C. baccatum, tomato, potato, and Arabidopsis MYBs spanning over 717 conserved syntenic segments. Using transcriptome data from three fruit developmental stages, a total of 54 CcMYBs and 81 CaMYBs showed significant differential expression patterns. Furthermore, the expression of 24 CcMYBs from the transcriptome data was validated by quantitative real-time (qRT) PCR analysis. Eight out of the 24 CcMYBs validated by the qRT-PCR were highly expressed in fiery hot C. chinense than in the lowly pungent C. annuum. Furthermore, the co-expression analysis revealed several MYB genes clustered with genes from the capsaicinoid, anthocyanin, phenylpropanoid, carotenoid, and flavonoids biosynthesis pathways, and related to determining fruit shape and size. The homology modeling of 126 R2R3 CcMYBs showed high similarity with that of the Arabidopsis R2R3 MYB domain template, suggesting their potential functional similarity at the proteome level. Furthermore, we have identified simple sequence repeat (SSR) motifs in the CcMYB genes, which could be used in Capsicum breeding programs. The functional roles of the identified CcMYBs could be studied further so that they can be manipulated for Capsicum trait improvement.

scholarly journals Genome-wide Characterization and Expression Analysis of YABBY Gene Family in Three Cultivars of Cucurbita Linn. And Their Response of Salt Stress in Cucurbita Moschata

2020 ◽  
Author(s):  
Jingping Yuan ◽  
Changwei Shen ◽  
Jingjing Xin ◽  
Zhenxia Li ◽  
Xinzheng Li ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Plant Growth ◽  
Gene Family ◽  
Expression Analysis ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Abiotic Stress Response ◽  
Element Analysis ◽  
Qrt Pcr

Abstract BackgroundPlant specific YABBY transcription factors have important biological roles in plant growth and abiotic stress. However, the identification of Cucurbita Linn. YABBY and their response to salt stress have not yet been reported. The gene number, gene distribution on chromosome, gene structure, protein conserved structure, protein motif and the cis-acting element of YABBY in three cultivars of Cucurbita Linn. were analyzed by bioinformatics tools, and their tissue expression patterns and expression profile under salt stress were analyzed.ResultsIn this study, 34 YABBY genes (11 CmoYABBYs in Cucurbita moschata, 12 CmaYABBYs in Cucurbita maxima, and 11 CpeYABBYs in Cucurbita pepo) were identified and they were divided into five subfamilies (YAB1/YAB3, YAB2, INO, CRC and YAB5). YABBYs in the same subfamily usually have similar gene structures (intron-exon distribution) and conserved domains. Chromosomal localization analysis showed that these CmoYABBYs, CmaYABBYs, and CpeYABBYs were unevenly distributed in 8, 9, and 9 chromosomes of 21 chromosomes, respectively. Total of 6 duplicated gene pairs, and they all experienced segmental duplication events. Cis-acting element analysis showed that some Cucurbita Linn. YABBYs were associated with at least one of plant hormone response, plant growth, and abiotic stress response. Transcriptional profiles of CmoYABBYs and CmaYABBYs in roots, stems, leaves, and fruits, and CpeYABBYs in seed and fruit mesocarp showed that YABBYs of Cucurbita Linn. had tissue specificity. Finally, the transcriptional profile of 11 CmoYABBYs in leaf and qRT-PCR analysis of CmoYABBYs in root under salt stress indicated that some genes may play an important role in salt stress.ConclusionsGenome-wide identification and expression analysis of YABBYs revealed the characteristics of YABBY gene family in three cultivars of Cucurbita Linn.. Transcriptome and qRT-PCR analysis revealed the response of the CmoYABBYs to salt stress.This provides a theoretical basis for the functional research and utilization of YABBY genes in Cucurbita Linn..

scholarly journals Selection and Validation of Reference Genes for qRT-PCR Analysis in the Oil-Rich Tuber Crop Tiger Nut (Cyperus esculentus) Based on Transcriptome Data

2021 ◽  
Vol 22 (5) ◽  
pp. 2569
Author(s):  
Xue Bai ◽  
Tao Chen ◽  
Yuan Wu ◽  
Mingyong Tang ◽  
Zeng-Fu Xu
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Cyperus Esculentus ◽  
Transcriptome Data ◽  
Qrt Pcr ◽  
Below Ground ◽  
The Stability

Tiger nut (Cyperus esculentus), a perennial C4 plant of the Cyperaceae family, is an unconventional crop that is distinguished by its oil-rich tubers, which also possesses the advantages of strong resistance, wide adaptability, short life periods, and large biomass. To facilitate studies on gene expression in this species, we identified and validated a series of reference genes (RGs) based on transcriptome data, which can be employed as internal controls for qRT-PCR analysis in tiger nut. Fourteen putative candidate RGs were identified and evaluated across nine different tissues of two cultivars, and the RGs were analyzed using three different algorithms (geNorm, NormFinder, and BestKeeper). The stability rankings of the candidate RGs were merged into consensus lists with RankAggreg. For the below-ground storage organ of tiger nut, the optimal RGs were TUB4 and UCE2 in different developmental stages of tubers. UCE2 and UBL5 were the most stably expressed RGs among all tissues, while Rubisco and PGK exhibited the lowest expression stability. UCE2, UBL5 and Rubisco were compared to normalize the expression levels of the caleosin (CLO) and diacylglycerol acyltransferase 2-2 (DGAT2-2) genes across the same tissues. Our results showed that the RGs identified in this study, which exhibit more uniform expression patterns, may be utilized for the normalization of qRT-PCR results, promoting further research on gene expression in various tissues of tiger nut.

scholarly journals Identification of Flower-Specific Promoters through Comparative Transcriptome Analysis in Brassica napus

2019 ◽  
Vol 20 (23) ◽  
pp. 5949 ◽  
Author(s):  
Yan Li ◽  
Caihua Dong ◽  
Ming Hu ◽  
Zetao Bai ◽  
Chaobo Tong ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Candidate Genes ◽  
Oilseed Rape ◽  
Agronomic Traits ◽  
Expression System ◽  
Expression Patterns ◽  
Gus Expression ◽  
Pcr Analysis ◽  
Transcriptome Data ◽  
Sclerotinia Stem Rot

Brassica napus (oilseed rape) is an economically important oil crop worldwide. Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum is a threat to oilseed rape production. Because the flower petals play pivotal roles in the SSR disease cycle, it is useful to express the resistance-related genes specifically in flowers to hinder further infection with S. sclerotiorum. To screen flower-specific promoters, we first analyzed the transcriptome data from 12 different tissues of the B. napus line ZS11. In total, 249 flower-specific candidate genes with high expression in petals were identified, and the expression patterns of 30 candidate genes were verified by quantitative real-time transcription-PCR (qRT-PCR) analysis. Furthermore, two novel flower-specific promoters (FSP046 and FSP061 promoter) were identified, and the tissue specificity and continuous expression in petals were determined in transgenic Arabidopsis thaliana with fusing the promoters to β-glucuronidase (GUS)-reporter gene. GUS staining, transcript expression pattern, and GUS activity analysis indicated that FSP046 and FSP061 promoter were strictly flower-specific promoters, and FSP046 promoter had a stronger activity. The two promoters were further confirmed to be able to direct GUS expression in B. napus flowers using transient expression system. The transcriptome data and the flower-specific promoters screened in the present study will benefit fundamental research for improving the agronomic traits as well as disease and pest control in a tissue-specific manner.

scholarly journals Commitment of Autologous Human Multipotent Stem Cells on Biomimetic Poly-L-Lactic Acid-Based Scaffolds Is Strongly Influenced by Structure and Concentration of Carbon Nanomaterial

Nanomaterials ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 415
Author(s):  
Marika Tonellato ◽  
Monica Piccione ◽  
Matteo Gasparotto ◽  
Pietro Bellet ◽  
Lucia Tibaudo ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Carbon Nanomaterials ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Marker Genes ◽  
Carbon Nanomaterial ◽  
Multipotent Stem Cells ◽  
Cell Lineages ◽  
Qrt Pcr ◽  
Nanocomposite Scaffolds

Nanocomposite scaffolds combining carbon nanomaterials (CNMs) with a biocompatible matrix are able to favor the neuronal differentiation and growth of a number of cell types, because they mimic neural-tissue nanotopography and/or conductivity. We performed comparative analysis of biomimetic scaffolds with poly-L-lactic acid (PLLA) matrix and three different p-methoxyphenyl functionalized carbon nanofillers, namely, carbon nanotubes (CNTs), carbon nanohorns (CNHs), and reduced graphene oxide (RGO), dispersed at varying concentrations. qRT-PCR analysis of the modulation of neuronal markers in human circulating multipotent cells cultured on nanocomposite scaffolds showed high variability in their expression patterns depending on the scaffolds’ inhomogeneities. Local stimuli variation could result in a multi- to oligopotency shift and commitment towards multiple cell lineages, which was assessed by the qRT-PCR profiling of markers for neural, adipogenic, and myogenic cell lineages. Less conductive scaffolds, i.e., bare poly-L-lactic acid (PLLA)-, CNH-, and RGO-based nanocomposites, appeared to boost the expression of myogenic-lineage marker genes. Moreover, scaffolds are much more effective on early commitment than in subsequent differentiation. This work suggests that biomimetic PLLA carbon-nanomaterial (PLLA-CNM) scaffolds combined with multipotent autologous cells can represent a powerful tool in the regenerative medicine of multiple tissue types, opening the route to next analyses with specific and standardized scaffold features.

scholarly journals Selection and validation of reference genes for normalization of qRT-PCR data to study secondary metabolite related genes in industrial hemp

2021 ◽  
Author(s):  
Michihito Deguchi ◽  
Shobha Potlakayala ◽  
Zachary Spuhler ◽  
Hannah George ◽  
Vijay Sheri ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heavy Metal ◽  
Expression Analysis ◽  
Reference Genes ◽  
Cannabis Sativa ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Qrt Pcr ◽  
Differential Gene ◽  
Industrial Hemp

Abstract Industrial hemp (Cannabis sativa L.) is a dioecious crop widely known for its production of phytocannabinoids, flavonoids, and terpenes. In the past two years since its legalization, there has been significant interest in researching this important crop for pharmaceutical applications. Although many scientific reports have demonstrated gene expression analysis of hemp through OMICs approaches, accurate validation of omics data cannot be performed because of lack of reliable reference genes for normalization of qRT-PCR data. The differential gene expression patterns of 13 candidate reference genes under osmotic, heavy metal, hormonal, and UV stress were evaluated through four software packages: geNorm, NormFinder, BestKeeper, and RefFinder. The EF-1a ranked as the most stable reference gene across all stresses, TUB was the most stable under osmotic stress, and TATA was the most stable under both heavy metal and hormonal stress. The expression profiles of two cannabinoid pathway genes, AAE1 and THCAS, using the two most stable and single least stable reference genes confirmed that two most stables genes were apt for normalization of gene expression data. This work will contribute to the future studies on the expression analysis of hemp genes regulating the synthesis, transport and accumulation of secondary metabolites.

scholarly journals Transcriptome and Gene Editing Analyses Reveal MOF1a Defect Alters the Expression of Genes Associated with Tapetum Development and Chromosome Behavior at Meiosis Stage Resulting in Low Pollen Fertility of Tetraploid Rice

2020 ◽  
Vol 21 (20) ◽  
pp. 7489
Author(s):  
Zijun Lu ◽  
Xiaotong Guo ◽  
Zhiyu Huang ◽  
Juan Xia ◽  
Xiang Li ◽  
...  
Keyword(s):  
Differential Expression ◽  
Pollen Development ◽  
Pollen Fertility ◽  
Expression Patterns ◽  
Middle Layer ◽  
Low Fertility ◽  
Myb Transcription Factor ◽  
Pcr Analysis ◽  
High Fertility ◽  
Autotetraploid Rice

Autotetraploid rice is a useful rice germplasm for polyploid rice breeding. However, low fertility limits its commercial production. A neo-tetraploid rice with high fertility was developed from the progenies of crossing between autotetraploid lines by our research group. Our previous study showed that a myeloblastosis (MYB) transcription factor, MOF1, might be associated with the pollen development in tetraploid rice. However, little information is available about its role in pollen development in tetraploid rice. Here, we identified a new haplotype of MOF1 from neo-tetraploid rice and marked it as MOF1a. Transcriptome and qRT-PCR analysis demonstrated that MOF1a highly expressed in anthers, and displayed differential expression in neo-tetraploid rice compared to tetraploid rice line with low pollen fertility. The mutant (mof1a) of MOF1a, which was generated by CRISPR/Cas9 knockout in neo-tetraploid rice, showed low pollen fertility, and also exhibited abnormal tapetum and middle layer development, and defective chromosome behaviors during meiosis. A total of 13 tapetal related genes were found to be up-regulated in meiotic anthers of MOF1a compared with wild type plants by RNA-seq analysis, including CYP703A3, PTC1, and OsABCG26, which had been demonstrated to affect tapetal development. Moreover, 335 meiosis-related genes displayed differential expression patterns at same stage, including nine important meiosis-related genes, such as metallothionein OsMT1a. These results demonstrated that MOF1a plays an important role in pollen development and provides a foundation for understanding the molecular mechanism underlying MOF1a in reproduction of tetraploid rice.

scholarly journals Selection and evaluation of reference genes for qRT-PCR analysis in Euscaphis konishii Hayata based on transcriptome data

Plant Methods ◽  
2018 ◽  
Vol 14 (1) ◽  
Author(s):  
Wenxian Liang ◽  
Xiaoxing Zou ◽  
Rebeca Carballar-Lejarazú ◽  
Lingjiao Wu ◽  
Weihong Sun ◽  
...  
Keyword(s):  
Reference Genes ◽  
Pcr Analysis ◽  
Transcriptome Data ◽  
Qrt Pcr

scholarly journals Reference gene selection for qRT-PCR assays inStellera chamaejasmesubjected to abiotic stresses and hormone treatments based on transcriptome datasets

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4535 ◽  
Author(s):  
Xin Liu ◽  
Huirui Guan ◽  
Min Song ◽  
Yanping Fu ◽  
Xiaomin Han ◽  
...  
Keyword(s):  
Gene Expression ◽  
Internal Control ◽  
Abiotic Stresses ◽  
Target Genes ◽  
Expression Patterns ◽  
Control Measures ◽  
Rapid Expansion ◽  
Pcr Analysis ◽  
Data Normalization ◽  
Qrt Pcr

BackgroundStellera chamaejasmeLinn, an important poisonous plant of the China grassland, is toxic to humans and livestock. The rapid expansion ofS. chamaejasmehas greatly damaged the grassland ecology and, consequently, seriously endangered the development of animal husbandry. To draft efficient prevention and control measures, it has become more urgent to carry out research on its adaptive and expansion mechanisms in different unfavorable habitats at the genetic level. Quantitative real-time polymerase chain reaction (qRT-PCR) is a widely used technique for studying gene expression at the transcript level; however, qRT-PCR requires reference genes (RGs) as endogenous controls for data normalization and only through appropriate RG selection and qRT-PCR can we guarantee the reliability and robustness of expression studies and RNA-seq data analysis. Unfortunately, little research on the selection of RGs for gene expression data normalization inS. chamaejasmehas been reported.MethodIn this study, 10 candidate RGs namely,18S,60S,CYP,GAPCP1,GAPDH2,EF1B,MDH,SAND,TUA1, andTUA6, were singled out from the transcriptome database ofS. chamaejasme, and their expression stability under three abiotic stresses (drought, cold, and salt) and three hormone treatments (abscisic acid, ABA; gibberellin, GA; ethephon, ETH) were estimated with the programs geNorm, NormFinder, and BestKeeper.ResultOur results showed thatGAPCP1andEF1Bwere the best combination for the three abiotic stresses, whereasTUA6andSAND,TUA1andCYP,GAPDH2and60Swere the best choices for ABA, GA, and ETH treatment, respectively. Moreover,GAPCP1and60Swere assessed to be the best combination for all samples, and18Swas the least stable RG for use as an internal control in all of the experimental subsets. The expression patterns of two target genes (P5CS2andGI) further verified that the RGs that we selected were suitable for gene expression normalization.DiscussionThis work is the first attempt to comprehensively estimate the stability of RGs inS. chamaejasme. Our results provide suitable RGs for high-precision normalization in qRT-PCR analysis, thereby making it more convenient to analyze gene expression under these experimental conditions.

scholarly journals Selection and Validation of Appropriate Reference Genes for qRT-PCR Analysis of Flowering Stages and Different Genotypes of Iris Germanica L.

2021 ◽  
Author(s):  
Yinjie Wang ◽  
Yongxia Zhang ◽  
Qingquan Liu ◽  
Haiying Tong ◽  
Ting Zhang ◽  
...  
Keyword(s):  
Reference Genes ◽  
Molecular Mechanisms ◽  
Gene Selection ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Herbaceous Plant ◽  
Flower Bud ◽  
Perennial Herbaceous Plant ◽  
Qrt Pcr ◽  
Iris Germanica

Abstract Iris germanica L. is a perennial herbaceous plant that has been widely cultivated worldwide and is popular for its elegant and vibrantly colorful flowers. Selection of appropriate reference genes is the prerequisite for accurate normalization of target gene expression by quantitative real-time PCR. However, to date, the most suitable reference genes for flowering stages have not been elucidated in I. germanica. In this study, eight candidate reference genes were examined for the normalization of qRT-PCR in three I. germanica cultivars, and their stability were evaluated by four different algorithms (GeNorm, NormFinder, BestKeeper, and Ref-finder). The results revealed that IgUBC and IgGAPDH were the most stable reference genes in ‘00246’ and ‘Elizabeth’, and IgTUB and IgUBC showed stable expression in ‘2010200’. IgUBC and IgGAPDH were the most stable in all samples, while IgUBQ showed the least stability. Finally, to validate the reliability of the selected reference genes, the expression patterns of IgFT (Flowering Locus T gene) was analyzed and emphasized the importance of appropriate reference gene selection. This work presented the first systematic study of reference genes selection during flower bud development and provided guidance to research of the molecular mechanisms of flowering stages in I. germanica.

scholarly journals Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Isaac M Chiu ◽  
Lee B Barrett ◽  
Erika K Williams ◽  
David E Strochlic ◽  
Seungkyu Lee ◽  
...  
Keyword(s):  
Clustering Analysis ◽  
Molecular Diversity ◽  
Transcriptional Profiling ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Molecular Signatures ◽  
Qrt Pcr ◽  
Somatosensory Neurons ◽  
Overlapping Classes ◽  
Somatosensory Nervous System

The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4+SNS-Cre/TdTomato+, 2) IB4−SNS-Cre/TdTomato+, and 3) Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation.

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