scholarly journals Genome-Wide Identification and Expression Analysis of the Ascorbate Oxidase Gene Family in Gossypium hirsutum Reveals the Critical Role of GhAO1A in Delaying Dark-Induced Leaf Senescence

2019 ◽  
Vol 20 (24) ◽  
pp. 6167
Author(s):  
Ze Pan ◽  
Lihua Chen ◽  
Fei Wang ◽  
Wangyang Song ◽  
Aiping Cao ◽  
...  
Keyword(s):  
Ascorbic Acid ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Leaf Senescence ◽  
Expression Patterns ◽  
Critical Role ◽  
Ascorbate Oxidase ◽  
Oxidase Gene ◽  
Increased Sensitivity ◽  
Functionally Diverse

Ascorbate oxidase (AO) plays important roles in plant growth and development. Previously, we reported a cotton AO gene that acts as a positive factor in cell growth. Investigations on Gossypium hirsutum AO (GhAO) family genes and their multiple functions are limited. The present study identified eight GhAO family genes and performed bioinformatic analyses. Expression analyses of the tissue specificity and developmental feature of GhAOs displayed their diverse expression patterns. Interestingly, GhAO1A demonstrated the most rapid significant increase in expression after 1 h of light recovery from the dark. Additionally, the transgenic ao1-1/GhAO1A Arabidopsis lines overexpressing GhAO1A in the Arabidopsis ao1-1 late-flowering mutant displayed a recovery to the normal phenotype of wild-type plants. Moreover, compared to the ao1-1 mutant, the ao1-1/GhAO1A transgenic Arabidopsis presented delayed leaf senescence that was induced by the dark, indicating increased sensitivity to hydrogen peroxide (H2O2) under normal conditions that might be caused by a reduction in ascorbic acid (AsA) and ascorbic acid/dehydroascorbate (AsA/DHA) ratio. The results suggested that GhAOs are functionally diverse in plant development and play a critical role in light responsiveness. Our study serves as a foundation for understanding the AO gene family in cotton and elucidating the regulatory mechanism of GhAO1A in delaying dark-induced leaf senescence.

scholarly journals Identification and Expression Profiling of Protein Phosphatases (PP2C) Gene Family in Gossypium hirsutum L.

2019 ◽  
Vol 20 (6) ◽  
pp. 1395 ◽  
Author(s):  
Hamna Shazadee ◽  
Nadeem Khan ◽  
Jingjing Wang ◽  
Chencan Wang ◽  
Jianguo Zeng ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Family ◽  
Expression Profiling ◽  
Critical Role ◽  
Fiber Development ◽  
Chromosomal Mapping ◽  
Composition Analysis ◽  
Specific Gene ◽  
Specific Response ◽  
Pp2c Gene

The protein phosphatase (PP2C) gene family, known to participate in cellular processes, is one of the momentous and conserved plant-specific gene families that regulate signal transduction in eukaryotic organisms. Recently, PP2Cs were identified in Arabidopsis and various other crop species, but analysis of PP2C in cotton is yet to be reported. In the current research, we found 87 (Gossypium arboreum), 147 (Gossypium barbadense), 181 (Gossypium hirsutum), and 99 (Gossypium raimondii) PP2C-encoding genes in total from the cotton genome. Herein, we provide a comprehensive analysis of the PP2C gene family in cotton, such as gene structure organization, gene duplications, expression profiling, chromosomal mapping, protein motif organization, and phylogenetic relationships of each species. Phylogenetic analysis further categorized PP2C genes into 12 subgroups based on conserved domain composition analysis. Moreover, we observed a strong signature of purifying selection among duplicated pairs (i.e., segmental and dispersed) of Gossypium hirsutum. We also observed the tissue-specific response of GhPP2C genes in organ and fiber development by comparing the RNA-sequence (RNA-seq) data reported on different organs. The qRT-PCR validation of 30 GhPP2C genes suggested their critical role in cotton by exposure to heat, cold, drought, and salt stress treatments. Hence, our findings provide an overview of the PP2C gene family in cotton based on various bioinformatic tools that demonstrated their critical role in organ and fiber development, and abiotic stress tolerance, thereby contributing to the genetic improvement of cotton for the resistant cultivar.

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.

scholarly journals Identification of the Golden-2-like transcription factors gene family in Gossypium hirsutum

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12484
Author(s):  
Zilin Zhao ◽  
Jiaran Shuang ◽  
Zhaoguo Li ◽  
Huimin Xiao ◽  
Yuling Liu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Response ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Abiotic Stress Response ◽  
Qrt Pcr

Background Golden2-Like (GLK) transcription factors are a type of transcriptional regulator in plants. They play a pivotal role in the plant physiological activity process and abiotic stress response. Methods In this study, the potential function of GLK family genes in Gossypium hirsutum was studied based on genomic identification, phylogenetic analysis, chromosome mapping and cis-regulatory elements prediction. Gene expression of nine key genes were analyzed by qRT-PCR experiments. Results Herein, we identified a total of 146 GhGLK genes in Gossypium hirsutum, which were unevenly distributed on each of the chromosomes. There were significant differences in the number and location of genes between the At sub-genome and the Dt sub-genome. According to the phylogenetic analysis, they were divided into ten subgroups, each of which had very similar number and structure of exons and introns. Some cis-regulatory elements were identified through promoter analysis, including five types of elements related to abiotic stress response, five types of elements related to phytohormone and five types of elements involved in growth and development. Based on public transcriptome data analysis, we identified nine key GhGLKs involved in salt, cold, and drought stress. The qRT-PCR results showed that these genes had different expression patterns under these stress conditions, suggesting that GhGLK genes played an important role in abiotic stress response. This study laid a theoretical foundation for the screening and functional verification of genes related to stress resistance of GLK gene family in cotton.

scholarly journals Identification and expression analysis of Tubulin gene family in upland cotton

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Baojun CHEN ◽  
Junjie ZHAO ◽  
Guoyong FU ◽  
Xinxin PEI ◽  
Zhaoe PAN ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Critical Role ◽  
Fiber Development ◽  
Pcr Analysis ◽  
Evolutionary Analysis ◽  
Tubulin Gene ◽  
Core Element ◽  
Protein Motifs ◽  
Seed Epidermis

Abstract Background Cotton fibers are single-celled extensions of the seed epidermis, a model tissue for studying cytoskeleton. Tubulin genes play a critical role in synthesizing the microtubules (MT) as a core element of the cytoskeleton. However, there is a lack of studies concerning the systematic characterization of the tubulin gene family in cotton. Therefore, the identification and portrayal of G. hirsutum tubulin genes can provide key targets for molecular manipulation in cotton breeding. Result In this study, we investigated all tubulin genes from different plant species and identified 98 tubulin genes in G. hirsutum. Phylogenetic analysis showed that tubulin family genes were classified into three subfamilies. The protein motifs and gene structure of α-, β-tubulin genes are more conserved compared with γ-tubulin genes. Most tubulin genes are located at the proximate ends of the chromosomes. Spatiotemporal expression pattern by transcriptome and qRT-PCR analysis revealed that 12 α-tubulin and 7 β-tubulin genes are specifically expressed during different fiber development stages. However, Gh.A03G027200, Gh.D03G169300, and Gh.A11G258900 had differential expression patterns at distinct stages of fiber development in varieties J02508 and ZRI015. Conclusion In this study, the evolutionary analysis showed that the tubulin genes were divided into three clades. The genetic structures and molecular functions were highly conserved in different plants. Three candidate genes, Gh.A03G027200, Gh.D03G169300, and Gh.A11G258900 may play a key role during fiber development complementing fiber length and strength.

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.

scholarly journals Genome-Wide Identification and Transcriptional Expression of the PAL Gene Family in Common Walnut (Juglans Regia L.)

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 46 ◽  
Author(s):  
Feng Yan ◽  
Huaizhu Li ◽  
Peng Zhao
Keyword(s):  
Gene Family ◽  
Juglans Regia ◽  
Expression Patterns ◽  
Critical Role ◽  
Phenylpropanoid Pathway ◽  
Transcriptional Expression ◽  
Genome Wide ◽  
A Genome ◽  
The Common ◽  
Common Walnut

Juglans regia L. is an economically important crop cultivated worldwide for its high quality and quantity of wood and nuts. Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway that plays a critical role in plant growth, development, and adaptation, but there have been few reports of the PAL gene family in common walnut. Here, we report a genome-wide study of J. regia PAL genes and analyze their phylogeny, duplication, microRNA, and transcriptional expression. A total of 12 PAL genes were identified in the common walnut and clustered into two subfamilies based on phylogenetic analysis. These common walnut PALs are distributed on eight different pseudo-chromosomes. Seven of the 12 PALs (JrPAL2-3, JrPAL4-2, JrPAL2-1, JrPAL4-1, JrPAL8, JrPAL9, and JrPAL6) were specific found in J. regia, and JrPAL3, JrPAL5, JrPAL1-2, JrPAL7, and JrPAL2-2 were found to be closely associated with the woody plant Populus trichocarpa. Additionally, the expression patterns of JrPAL3, JrPAL7, JrPAL9, and JrPAL2-1 showed that they had high expression in female and male flowers. The miRNA ath-miR830-5p regulates two genes, JrPAL5 and JrPAL1, such that they have low expression in the male and female flowers of the common walnut. Our research provides useful information for further research into the function of PAL genes in common walnut and Juglans.

scholarly journals Identification and Analysis of GhEXO Gene Family Indicated That GhEXO7_At Promotes Plant Growth and Development Through Brassinosteroid Signaling in Cotton (Gossypium hirsutum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Shengdong Li ◽  
Zhao Liu ◽  
Guoquan Chen ◽  
Ghulam Qanmber ◽  
Lili Lu ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Growth And Development ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Virus Induced Gene Silencing ◽  
Plant Growth And Development ◽  
Altered Expression ◽  
Protein Motifs

Brassinosteroids (BRs), an efficient plant endogenous hormone, significantly promotes plant nutrient growth adapting to biological and abiotic adversities. BRs mainly promote plant cell elongation by regulating gene expression patterns. EXORDIUM (EXO) genes have been characterized as the indicators of BR response genes. Cotton, an ancient crop, is of great economic value and its fibers can be made into all kinds of fabrics. However, EXO gene family genes have not been full identified in cotton. 175 EXO genes were identified in nine plant species, of which 39 GhEXO genes in Gossypium hirsutum in our study. A phylogenetic analysis grouped all of the proteins encoded by the EXO genes into five major clades. Sequence identification of conserved amino acid residues among monocotyledonous and dicotyledonous species showed a high level of conservation across the N and C terminal regions. Only 25% the GhEXO genes contain introns besides conserved gene structure and protein motifs distribution. The 39 GhEXO genes were unevenly distributed on the 18 At and Dt sub-genome chromosomes. Most of the GhEXO genes were derived from gene duplication events, while only three genes showed evidence of tandem duplication. Homologous locus relationships showed that 15 GhEXO genes are located on collinear blocks and that all orthologous/paralogous gene pairs had Ka &gt; Ks values, indicating purifying selection pressure. The GhEXO genes showed ubiquitous expression in all eight tested cotton tissues and following exposure to three phytohormones, IAA, GA, and BL. Furthermore, GhEXO7_At was mainly expressed in response to BL treatment, and was predominantly expressed in the fibers. GhEXO7_At was found to be a plasma membrane protein, and its ectopic expression in Arabidopsis mediated BR-regulated plant growth and development with altered expression of DWF4, CPD, KCS1, and EXP5. Additionally, the functions of GhEXO7_At were confirmed by virus-induced gene silencing (VIGS) in cotton. This study will provide important genetic resources for future cotton breeding programs.

Suppressed Expression of Ascorbate Oxidase Gene Promotes Ascorbic Acid Accumulation in Tomato Fruit

2010 ◽  
Vol 29 (3) ◽  
pp. 638-645 ◽  
Author(s):  
Yuyang Zhang ◽  
Hanxia Li ◽  
Wenbo Shu ◽  
Chanjuan Zhang ◽  
Wei Zhang ◽  
...  
Keyword(s):  
Ascorbic Acid ◽  
Tomato Fruit ◽  
Ascorbate Oxidase ◽  
Oxidase Gene ◽  
Acid Accumulation

scholarly journals Genome-Wide Study of the GATL Gene Family in Gossypium hirsutum L. Reveals that GhGATL Genes Act on Pectin Synthesis to Regulate Plant Growth and Fiber Elongation

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 64
Author(s):  
Lei Zheng ◽  
Huanhuan Wu ◽  
Ghulam Qanmber ◽  
Faiza Ali ◽  
Lingling Wang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gossypium Hirsutum ◽  
Positive Selection ◽  
Gene Family ◽  
Selection Pressure ◽  
Expression Patterns ◽  
Control Plant ◽  
Segmental Duplications ◽  
Fiber Elongation ◽  
Virus Induced Gene Silencing

Pectin is a major polysaccharide component that promotes plant growth and fiber elongation in cotton. In previous studies, the galacturonosyltransferase-like (GATL) gene family has been shown to be involved in pectin synthesis. However, few studies have been performed on cotton GATL genes. Here, a total of 33, 17, and 16 GATL genes were respectively identified in Gossypium hirsutum, Gossypium raimondii, and Gossypium arboreum. In multiple plant species, phylogenetic analysis divided GATL genes into five groups named GATL-a to GATL-e, and the number of groups was found to gradually change over evolution. Whole genome duplication (WGD) and segmental duplication played a significant role in the expansion of the GATL gene family in G. hirsutum. Selection pressure analyses revealed that GATL-a and GATL-b groups underwent a great positive selection pressure during evolution. Moreover, the expression patterns revealed that most of highly expressed GhGATL genes belong to GATL-a and GATL-b groups, which have more segmental duplications and larger positive selection value, suggesting that these genes may play an important role in the evolution of cotton plants. We overexpressed GhGATL2, GhGATL9, GhGATL12, and GhGATL15 in Arabidopsis and silenced the GhGATL15 gene in cotton through a virus induced gene silencing assay (VIGS). The transgenic and VIGS lines showed significant differences in stem diameter, epidermal hair length, stamen length, seed size, and fiber length than the control plant. In addition, the pectin content test proved that the pectin was significantly increased in the transgenic lines and reduced in VIGS plants, demonstrating that GhGATL genes have similar functions and act on the pectin synthesis to regulate plant growth and fiber elongation. In summary, we performed a comprehensive analysis of GhGATL genes in G. hirsutum including evolution, structure and function, in order to better understand GhGATL genes in cotton for further studies.

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