Nuclear Factor-Y (NF-Y), the Key Player in Plant Growth and Development: Prediction and Characterization in Vanilla planifolia

2020 ◽  
Vol 09 ◽  
Author(s):  
Saavi Arora ◽  
Devina Ghai ◽  
Jaspreet K Sembi
Keyword(s):  
Gene Family ◽  
Growth And Development ◽  
Functional Characterization ◽  
Evolutionary Relationship ◽  
Dimensional Structure ◽  
Evolutionary Analysis ◽  
Nuclear Factor ◽  
Vanilla Planifolia ◽  
Variable Expression ◽  
Nuclear Factor Y

Background: V. planifolia is of tremendous commercial importance as a source of an important flavor, vanilla, which is the backbone of the culinary and perfumery industry. Hence, efforts to ease cultivation and promote growth in this plant are need of the hour. Nuclear factor-Y (NF-Y) gene family, a class of vital transcription factors, plays a pivotal role in a large number of developmental processes. Objectives: The present study aims to identify and characterize NF-Y gene family in Vanilla planifolia which would bring insights to their role as key factors promoting growth and development in this orchid. Methods: Physico-chemical characterization, protein structure prediction and interaction, establishment of evolutionary relationship and expression profiling were attempted using various in silico tools. Results: Twenty five putative NF-Y members were identified in Vanilla planifolia, which were further classified into three sub-classes, NF-YA (13), NF-YB (7) and NF-YC (5), on the basis of specific domains and conserved regions. Prediction of three dimensional structure was done on the basis of structural similarity with NF-Y structure templates. Evolutionary analysis with the NF-Ys of Arabidopsis thaliana and Oryza sativa, classified these into three major clusters which indicated towards similarity of functions. Variable expression of VpNF-Y genes confirmed their role in diverse functions. VpNF-YA genes generally showed higher expression in vegetative tissues while a few VpNF-YBs showed seed specific expression. Protein-protein interaction indicated complex formation for optimum function. Conclusions: This work paves way for further functional characterization of NF-Y genes in Vanilla planfolia.

scholarly journals Carotenoid Cleavage Dioxygenases: Identification, Expression, and Evolutionary Analysis of This Gene Family in Tobacco

2019 ◽  
Vol 20 (22) ◽  
pp. 5796
Author(s):  
Qianqian Zhou ◽  
Qingchang Li ◽  
Peng Li ◽  
Songtao Zhang ◽  
Che Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Physiological Stress ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Hormone Treatment ◽  
Nicotiana Sylvestris ◽  
Regulatory Elements ◽  
Evolutionary Analysis ◽  
Comprehensive Overview ◽  
Carotenoid Cleavage Dioxygenases

Carotenoid cleavage dioxygenases (CCDs) selectively catalyze carotenoids, forming smaller apocarotenoids that are essential for the synthesis of apocarotenoid flavor, aroma volatiles, and phytohormone ABA/SLs, as well as responses to abiotic stresses. Here, 19, 11, and 10 CCD genes were identified in Nicotiana tabacum, Nicotiana tomentosiformis, and Nicotiana sylvestris, respectively. For this family, we systematically analyzed phylogeny, gene structure, conserved motifs, gene duplications, cis-elements, subcellular and chromosomal localization, miRNA-target sites, expression patterns with different treatments, and molecular evolution. CCD genes were classified into two subfamilies and nine groups. Gene structures, motifs, and tertiary structures showed similarities within the same groups. Subcellular localization analysis predicted that CCD family genes are cytoplasmic and plastid-localized, which was confirmed experimentally. Evolutionary analysis showed that purifying selection dominated the evolution of these genes. Meanwhile, seven positive sites were identified on the ancestor branch of the tobacco CCD subfamily. Cis-regulatory elements of the CCD promoters were mainly involved in light-responsiveness, hormone treatment, and physiological stress. Different CCD family genes were predominantly expressed separately in roots, flowers, seeds, and leaves and exhibited divergent expression patterns with different hormones (ABA, MeJA, IAA, SA) and abiotic (drought, cold, heat) stresses. This study provides a comprehensive overview of the NtCCD gene family and a foundation for future functional characterization of individual genes.

scholarly journals Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7950 ◽  
Author(s):  
Yongbin Wang ◽  
Lei Ling ◽  
Zhenfeng Jiang ◽  
Weiwei Tan ◽  
Zhaojun Liu ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Growth And Development ◽  
Genomic Data ◽  
Evolutionary Analysis ◽  
Rna Seq ◽  
Plant Growth And Development ◽  
Genome Wide ◽  
Gene Structures

In eukaryotes, proteins encoded by the 14-3-3 genes are ubiquitously involved in the plant growth and development. The 14-3-3 gene family has been identified in several plants. In the present study, we identified 22 GmGF14 genes in the soybean genomic data. On the basis of the evolutionary analysis, they were clustered into ε and non-ε groups. The GmGF14s of two groups were highly conserved in motifs and gene structures. RNA-seq analysis suggested that GmGF14 genes were the major regulator of soybean morphogenesis. Moreover, the expression level of most GmGF14s changed obviously in multiple stress responses (drought, salt and cold), suggesting that they have the abilities of responding to multiple stresses. Taken together, this study shows that soybean 14-3-3s participate in plant growth and can response to various environmental stresses. These results provide important information for further understanding of the functions of 14-3-3 genes in soybean.

scholarly journals Genome-wide identification, phylogeny and expression analysis of G6PC gene family in common carp, Cyprinus carpio

2020 ◽  
Vol 45 (2) ◽  
Author(s):  
Sijia Liu ◽  
Fei Tian ◽  
Cunfang Zhang ◽  
Zhigang Qiao ◽  
Kai Zhao
Keyword(s):  
Gene Family ◽  
Common Carp ◽  
Cyprinus Carpio ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Critical Role ◽  
Cold Treatment ◽  
Evolutionary Relationship ◽  
Whole Genome Sequence ◽  
Evolutionary Analysis

AbstractObjectiveThe Glucose 6-phosphatase (G6Pase) catalytic subunit (G6PC) catalyzes glucose 6-phosphate (G6P) to inorganic phosphate and glucose, playing a critical role in endogenous energy supply. Here, the G6PC gene family was investigated and characterized in common carp (Cyprinus carpio).MethodsSequence alignment and phylogenetic analysis were performed using MEGA5. The HMM profiles, motif structure were analyzed using Pfam and MEME, respectively. Quantitative real-time PCR was used to test the expression profiles.ResultsFour assumptive members of G6PC family in common carp whole-genome sequence were identified as cg6pca.1, cg6pca.2a, cg6pca.2b and cg6pcb which were classified into g6pca and g6pcb subtypes, respectively. Evolutionary analysis revealed that cg6pca.2a and cg6pca.2b have a closer evolutionary relationship, and the same subtype members have higher homology among different species. A classical PAP2-glucose phosphates domain is found in four genes and were highly conserved. The expression patterns revealed that only cg6pca.2a elevated significantly after 12 and 24 h of both starvation and cold treatment (p < 0.05).ConclusionsThis study performed a comprehensive analysis of G6PC gene family in common carp. Moreover, cg6pca.2 may be the major functional gene in cold and fasting stress. And the transfactors, PLAG1 and Sox8, may be concerned with expression regulation of cg6pca.2.

GENOME-WIDE IDENTIFICATION AND COMPUTATIONAL CHARACTERIZATION OF THE NUCLEAR FACTOR-YC SUB-UNITS IN GRAIN AMARANTH (Amaranthus hypochondriacus)

2021 ◽  
Vol 66 (3) ◽  
pp. 161-169
Author(s):  
Huyen Tran Thi Thanh ◽  
Hong La Viet ◽  
Quynh Le Thi Ngoc ◽  
Thuy Pham Chau ◽  
Quyen Ha Thi ◽  
...  
Keyword(s):  
Growth And Development ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Chemical Properties ◽  
Nuclear Factor ◽  
Grain Amaranth ◽  
Amaranthus Hypochondriacus ◽  
Grand Average ◽  
Genes Encoding

Nuclear factor-Y (NF-Y) has been known as one of the plant-specific transcription factors that play key roles in numerous biological processes during the growth and development of plant species. In this study, a comprehensive analysis of NF-YC sub-units in grain amaranth (Amaranthus hypochondriacus) was carried out based on the bioinformatics approaches. Firstly, a total of five members of the NF-YC sub-units was reported in the grain amaranth. Its structural analyses revealed that the NF-YC sub-units were variable in physic-chemical properties, like protein sizes, molecular masses, isoelectric point, instability index, and grand average of hydropathy. Of our interest, the expression profiles of genes encoding NF-YC sub-units in various tissues\organs during the growth and development of grain amaranth. We found that three genes, including AhNF-YC01, AhNF-YC04, and AhNF-YC05 were highly expressed in leaf, root, floral, immature seed, and stem tissues. Interestingly, AhNF-YC05 was exclusively expressed in leaf and stem tissues. Taken together, our study could provide a solid understanding for further functional characterization of genes encoding NF-YC sub-units in grain amaranth.

scholarly journals Genome-wide identification and expression analysis of CYP450 gene family in Cucumis sativus L.

2021 ◽  
Author(s):  
hongyu wang ◽  
Pengfei Li ◽  
Yu Wang ◽  
Chunyu Chi ◽  
Guohua Ding
Keyword(s):  
Subcellular Localization ◽  
Gene Family ◽  
Cucumis Sativus ◽  
Expression Profile ◽  
Evolutionary Relationship ◽  
Evolutionary Analysis ◽  
Cucumis Sativus L ◽  
P450 Gene ◽  
Genome Wide ◽  
A Genome

Abstract The cytochrome P450 (CYP450) gene family plays a vital role in basic metabolism and enhances plant resistance to stress and pests. However, little information is available on the genome-wide characterization and evolutionary relationship of the CYP450 gene family in Cucumis sativus L. In the present study, a genome-wide bioinformatics analysis was performed, including gene structure, conserved motif, cis-acting promoter element, evolutionary analysis, collinearity, subcellular localization, and expression profile. The gene expression profile of CYP450 was verified using transcriptome sequencing and quantitative reverse transcription polymerase chain reaction. A total of 165 P450 genes were identified in the cucumber genome. These genes were classified into eight subfamilies and unevenly distributed on seven chromosomes. Subcellular localization predicted that most of P450 genes were located in chloroplasts and a few were located on the plasma membrane. CYP450 genes were differentially expressed in different tissues and in response to salicylic acid (SA) treatment. The sizes of all cucumber P450 proteins ranged from 317 to 1,056 aa, the theoretical isoelectric points ranged from 5.05 to 10.31, and the molecular weights ranged from 36,095 to 121,403 KD. This study provides a theoretical basis for further research on the biological functions of the P450 gene in cucumber plants.

scholarly journals Genomic Organization, Phylogenetic Comparison, and Differential Expression of the Nuclear Factor-Y Gene Family in Apple (Malus Domestica)

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 16
Author(s):  
Yanjie Qu ◽  
Yaping Wang ◽  
Jun Zhu ◽  
Yugang Zhang ◽  
Hongmin Hou
Keyword(s):  
Abiotic Stress ◽  
Malus Domestica ◽  
Growth And Development ◽  
Expression Patterns ◽  
Specific Response ◽  
Nuclear Factor ◽  
Element Analysis ◽  
Nuclear Factor Y ◽  
Gene Structures ◽  
Y Family

The nuclear factor Y (NF-Y) as a transcription factor plays an important role in plants growth and development, and response to stress. However, few genome-wide analyzes and functional research of the NF-Y family has been undertaken in apple (Malus domestica Borkh.) so far. In this study, we comprehensively identified the 43 MdNF-Y genes in apple, which dispersedly distributed among the three subgroups based on their sequence alignment analysis, including 11 MdNF-YAs, 22 MdNF-YBs and 10 MdNF-YCs. The members in the same subgroups had similar evolution relationships, gene structures, and conserved motifs. The gene duplication analysis suggested that all the genes were dispersed followed by 27 segmental duplication. Moreover, based on synteny analysis of MdNF-Ys with eight plant species results suggested that some ortholog genes were preserved during the evolution of these species. Cis-element analysis showed potential functions of MdNF-Ys in apple growth and development and responded to abiotic stress. Furthermore, the interaction among MdNF-Ys protein were investigated in yeast two-hybrid assays. The expression patterns of MdNF-Ys in tissue-specific response reveled divergence and might play important role in apple growth and development. Subsequently, whole MdNF-Y genes family was carried out for RT-PCR in response to five abiotic stress (ABA, drought, heat, cold, and salinity) to identify their expression patterns. Taken together, our study will provide a foundation for the further study to the molecular mechanism of apple in growing development and response to abiotic stresses.

scholarly journals In silico identification, characterization and expression profile of WUSCHEL-related homeobox (WOX) gene family in Vanilla planifolia

2020 ◽  
Vol 7 (2) ◽  
pp. 206-213
Author(s):  
Thiveyarajan Victorathisayam ◽  
Madhvi Kanchan ◽  
` Himani ◽  
Thandullu R. Suriyanarayanan ◽  
Jaspreet K. Sembi ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profile ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Alpha Helix ◽  
Vanilla Planifolia ◽  
In Planta ◽  
Specific Expression ◽  
Spatio Temporal

Vanilla planifolia is an economically important orchid, which is being commercially exploited by the food industry for the highly valued secondary metabolite vanillin. WUSCHEL-related homeobox (WOX) gene family encodes for WUSCHEL-related homeobox (WOX) transcription factors that participate in embryogenesis, organogenesis and florigenesis and in diverse plant developmental processes as well. In the present study, we analysed V. planifolia transcriptome and identified 6 WOX (VpWOX) transcripts, that encode putative WOX (VpWOX) transcription factor proteins. Domain analysis was done which indicates the presence of helix-loop-helix-turn-helix which is identifying feature of WOX gene family proteins. We executed phylogenetic clustering for the VpWOX proteins with their counterpart from the model plant Arabidopsis thaliana (AtWOX) and other closely related orchid species, Phalaenopsis equestris (PeWOX), Dendrobium catenatum (DcWOX) and Apostasia shenzhenica (AsWOX) and established their clade specific grouping. Spatio-temporal expression profile for VpWOX genes was analysed for different plant developmental stages which shows that VpWOX13 is expressing uniformly in all the developmental stages whereas, other genes have tissue specific expression. Based on gene expression patterns, we selected four VpWOX proteins and carried out secondary and tertiary structural analysis which indicates the presence of alpha helix and beta turn in the protein structure. The present study provides basic understanding of the functioning of WOX gene family in V. planifolia and paves the path for functional characterization of selected VpWOX genes in planta and in heterologous system in future for commercial utilization.

scholarly journals Genome-Wide Analysis of the Thioredoxin Gene Family in Gossypium hirsutum L. and the Role of the Atypical Thioredoxin Gene GhTRXL3-2 in Flowering

2021 ◽  
Author(s):  
Hui Liu ◽  
Yunfei Li ◽  
Xianzhong Huang
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Family ◽  
Growth And Development ◽  
Structural Characteristics ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Whole Genome Sequence ◽  
Evolutionary Analysis ◽  
Specific Expression ◽  
Flowering Regulation

AbstractThioredoxin (TRX) is a highly conserved low-molecular-weight protein and a ubiquitous antioxidant enzyme that plays key role in the regulation of plant growth and development. Here, using the whole-genome sequence, we performed a systematic analysis for the TRX gene family in upland cotton (Gossypium hirsutum L.) and analyzed their structural characteristics, evolution, and expression profiles during growth and development. At least 86 GhTRX members, 40 typical and 46 atypical, were identified in the cotton genome, and they were unevenly distributed on the 26 chromosomes. Conserved domains and phylogenic tree construction classified the typical TRX gene family into seven subfamilies and the atypical TRX into nine subfamilies. An evolutionary analysis revealed that the TRX gene family underwent purification selection during evolution. In addition, an RNA-Seq analysis showed that, during vegetative and reproductive development, the differences in transcript abundance levels and organ-specific expression patterns suggest functional diversity. Biochemical assays demonstrated that the atypical TRX protein GhTRXL3-2 interacted with the cotton FLOWERING LOCUS T protein GhFT. The overexpression of GhTRXL3-2 in Arabidopsis thaliana resulted in early flowering compared with control plants. Additionally, the silencing of GhTRXL3-2 in cotton delayed maturation, suggesting that it has important roles in cotton’s flowering regulation. These results help clarify the evolution of the TRX genes and elucidate their biological functions in cotton flowering regulation.

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