Identification and Expression Analysis of the PIN and AUX/LAX Gene Families in Ramie (Boehmeria nivea L. Gaud)

Auxin regulates diverse aspects of growth and development. Furthermore, polar auxin transport, which is mediated by the PIN-FORMED (PIN) and AUXIN1/LIKE-AUX (AUX/LAX) proteins, plays a crucial role in auxin distribution. In this study, six PIN and four AUX/LAX genes were identified in ramie (Boehmeria nivea L.). We used qRT-PCR to characterize and analyze the two gene families, including phylogenetic relationships, intron/exon structures, cis-elements, subcellular localization, and the expression patterns in different tissues. The expression of these genes in response to indole-3-acetic acid (IAA) treatment and drought stress was also assessed; the results indicate that most of the BnAUX/LAX and BnPIN genes were regulated as a result of IAA treatment and drought stress. Our study provides insights into ramie auxin transporters and lays the foundation for further analysis of their biological functions in ramie fiber development and adaptation to environmental stresses.

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Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

10.7287/peerj.preprints.27819 ◽

2019 ◽

Author(s):

Yong Zhou ◽

Yuan Cheng ◽

Chunpeng Wan ◽

Youxin Yang ◽

Jinyin Chen

Keyword(s):

Phylogenetic Analysis ◽

Gene Family ◽

Expression Patterns ◽

Future Research ◽

Biological Processes ◽

Biological Functions ◽

Specific Expression ◽

Qrt Pcr ◽

Genome Wide ◽

Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and response to stresses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon-intron structure. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of the nine selected ClDof genes under salt stress and ABA treatments using qRT-PCR, and they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

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Evolution of Acyl-CoA-binding protein gene family in plants provides insights into potential functions of grapevine (Vitis vinifera L.)

Journal of Berry Research ◽

10.3233/jbr-200528 ◽

2020 ◽

Vol 10 (4) ◽

pp. 677-696

Author(s):

Zhi-Gang Dong ◽

Hui Liu ◽

Xiao-Long Wang ◽

Jun Tang ◽

Kai-Kai Zhu ◽

...

Keyword(s):

Drought Stress ◽

Gene Family ◽

Microarray Data ◽

Expression Profiles ◽

Functional Divergence ◽

Expression Patterns ◽

Potential Functions ◽

Physiological Data ◽

Structural Annotation ◽

Qrt Pcr

BACKGROUND: Grapevine was one of the most important perennial fruit crops worldwide. Acyl-CoA-binding proteins (ACBPs) in eudicots and monocots show conservation in an acyl-CoA-binding domain (ACB domain) which binds acyl-CoA esters. OBJECTIVE: The information and data provided in the present study contributes to understand the evolutionary processes and potential functions of this gene family in grapevine growth and development, and responses to abiotic stress. METHODS: Using the complete grapevine genome sequences, we investigated the number grapevine ACBP genes, the exon-intron structure, phylogenetic relationships and synteny with the Arabidopsis ACBP gene family. Furthermore, the expression profiles of VvACBP genes based on public microarray data in different tissues, and the expression patterns responding to different exogenous hormones as well as abiotic and biotic stresses were presented. The qRT-PCR was used to verify the microarray data under drought stress treatments. Finally, the leaf relative water content (RWC), leaf chlorophyll content, and enzymatic activities were measured to further examine the tolerance to drought stress in grapevine. RESULTS: The six grapevine ACBPs were identified. Their distribution into various groups differed from Arabidopsis and rice. Synteny analysis demonstrated that several VvACBP genes were found in corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of the respective lineages. Sequence alignment and structural annotation provided an overview of variations that might contribute to functional divergence from Arabidopsis ACBPs. Expressional analyses suggested that both conserved and variant biological functions exist in ACBPs across different species. The expression pattern of these genes were similar in the microarray and qRT-PCR analyses. Gene structure organization and expression characteristics of VvACBPs resembled those of their Arabidopsis orthologous, although species-specific differences also exist. Differential regulation of genes suggested functional diversification among isoforms. The biochemical and physiological data showed the tolerance to drought stress of grapevine. CONCLUSIONS: These findings provided insight into evolution of ACBP gene family in plants and a solid foundation for a deeper understanding of the complex molecular responses of grapevine to stress.

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Genome-Wide Identification and Characterization of PIN-FORMED (PIN) Gene Family Reveals Role in Developmental and Various Stress Conditions in Triticum aestivum L.

International Journal of Molecular Sciences ◽

10.3390/ijms22147396 ◽

2021 ◽

Vol 22 (14) ◽

pp. 7396

Author(s):

Manu Kumar ◽

Bhagwat Singh Kherawat ◽

Prajjal Dey ◽

Debanjana Saha ◽

Anupama Singh ◽

...

Keyword(s):

Gene Family ◽

Auxin Transport ◽

Expression Patterns ◽

Triticum Aestivum L ◽

Stress Conditions ◽

Biotic And Abiotic Stress ◽

Developmental Processes ◽

Qrt Pcr ◽

Genome Wide

PIN-FORMED (PIN) genes play a crucial role in regulating polar auxin distribution in diverse developmental processes, including tropic responses, embryogenesis, tissue differentiation, and organogenesis. However, the role of PIN-mediated auxin transport in various plant species is poorly understood. Currently, no information is available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the PIN gene family in wheat to understand the evolution of PIN-mediated auxin transport and its role in various developmental processes and under different biotic and abiotic stress conditions. In this study, we performed genome-wide analysis of the PIN gene family in common wheat and identified 44 TaPIN genes through a homology search, further characterizing them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses led to the classification of TaPIN genes into seven different groups, providing evidence of an evolutionary relationship with Arabidopsis thaliana and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, transmembrane domains, and three-dimensional (3D) structure were also examined using various computational approaches. Cis-elements analysis of TaPIN genes showed that TaPIN promoters consist of phytohormone, plant growth and development, and stress-related cis-elements. In addition, expression profile analysis also revealed that the expression patterns of the TaPIN genes were different in different tissues and developmental stages. Several members of the TaPIN family were induced during biotic and abiotic stress. Moreover, the expression patterns of TaPIN genes were verified by qRT-PCR. The qRT-PCR results also show a similar expression with slight variation. Therefore, the outcome of this study provides basic genomic information on the expression of the TaPIN gene family and will pave the way for dissecting the precise role of TaPINs in plant developmental processes and different stress conditions.

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Auxin-induced developmental patterns in Brassica juncea embryos

Development ◽

10.1242/dev.125.5.879 ◽

1998 ◽

Vol 125 (5) ◽

pp. 879-887 ◽

Cited By ~ 7

Author(s):

K. Hadfi ◽

V. Speth ◽

G. Neuhaus

Keyword(s):

Brassica Juncea ◽

Auxin Transport ◽

Developmental Patterns ◽

Globular Embryos ◽

Auxin Distribution ◽

Wide Range ◽

Auxin Transport Inhibitor ◽

Indole 3 Acetic Acid ◽

Chlorophenoxyisobutyric Acid

To investigate the mechanism of auxin action during pattern formation in dicot embryos, we tested the effects of the natural auxin indole-3-acetic acid (IAA), the auxin transport inhibitor N-(1-naphthyl)thalamic acid (NPA) and the antiauxin p-chlorophenoxyisobutyric acid (PCIB). In vitro treatments of isolated zygotic Brassica juncea embryos with these substances led to a wide range of morphogenetic alterations. Treatment of globular embryos with exogenous auxin (10-40 microM) either completely inhibited morphogenesis, resulting in ball-shaped embryos, or caused the development of egg- and cucumber-shaped embryos, which only consisted of a shortened hypocotyl without any apical structures. Axis duplication was observed sometimes after inhibition of auxin transport in globular embryos, and led to the development of twin embryos. During the transition from globular to heart stage, changes in auxin distribution or activity frequently caused the development of either split-collar or collar-cotyledons. Antiauxin inhibited cotyledon growth, leading to embryos with single or no cotyledons, or inhibited the development of the hypocotyl and the radicle. Inhibition of auxin transport in transition embryos sometimes led to axis broadening, which resulted in the development of two radicles. The described changes in embryo shapes represent arrests in different auxin-regulated developmental steps and phenocopy some Arabidopsis morphogenetic mutants.

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Genome-wide analysis of BpDof genes and the tolerance to drought stress in birch (Betula platyphylla)

PeerJ ◽

10.7717/peerj.11938 ◽

2021 ◽

Vol 9 ◽

pp. e11938

Author(s):

Shilin Sun ◽

Bo Wang ◽

Qi Jiang ◽

Zhuoran Li ◽

Site Jia ◽

...

Keyword(s):

Drought Stress ◽

Gene Family ◽

Expression Patterns ◽

Structure Evolution ◽

Gene Gain ◽

Betula Platyphylla ◽

Ros Scavenging ◽

Promoter Regions ◽

Chromosomal Distribution ◽

Qrt Pcr

Background DNA binding with one finger (Dof) proteins are plant-specific transcription factors playing vital roles in developmental processes and stress responses in plants. Nevertheless, the characterizations, expression patterns, and functions of the Dof family under drought stress (a key determinant of plant physiology and metabolic homeostasis) in woody plants remain unclear. Methods The birch (Betula platyphylla var. mandshuric) genome and plant TFDB database were used to identify Dof gene family members in birch plants. ClustalW2 of BioEdit v7.2.1, MEGA v7.0, ExPASy ProtParam tool, Subloc, TMHMM v2.0, GSDS v2.0, MEME, TBtools, KaKs Calculator v2.0, and PlantCARE were respectively used to align the BpDof sequences, build a phylogenetic tree, identify the physicochemical properties, analyze the chromosomal distribution and synteny, and identify the cis-elements in the promoter regions of the 26 BpDof genes. Additionally, the birch seedlings were exposed to PEG6000-simulated drought stress, and the expression patterns of the BpDof genes in different tissues were analyzed by qRT-PCR. The histochemical staining and the evaluation of physiological indexes were performed to assess the plant tolerance to drought with transient overexpression of BpDof4, BpDof11, and BpDof17 genes. SPSS software and ANOVA were used to conduct all statistical analyses and determine statistically significant differences between results. Results A total of 26 BpDof genes were identified in birch via whole-genome analysis. The conserved Dof domain with a C(x)2C(x)21C(x)2C zinc finger motif was present in all BpDof proteins. These birch BpDofs were classified into four groups (A to D) according to the phylogenetic analysis of Arabidopsis thaliana Dof genes. BpDof proteins within the same group mostly possessed similar motifs, as detected by conserved motif analysis. The exon–intron analysis revealed that the structures of BpDof genes differed, indicating probable gene gain and lose during the BpDof evolution. The chromosomal distribution and synteny analysis showed that the 26 BpDofs were unevenly distributed on 14 chromosomes, and seven duplication events among six chromosomes were found. Cis-acting elements were abundant in the promoter regions of the 26 BpDof genes. qRT-PCR revealed that the expression of the 26 BpDof genes was differentially regulated by drought stress among roots, stems, and leaves. Most BpDof genes responded to drought stress, and BpDof4, BpDof11, and BpDof17 were significantly up-regulated. Therefore, plants overexpressing these three genes were generated to investigate drought stress tolerance. The BpDof4-, BpDof11-, and BpDof17-overexpressing plants showed promoted reactive oxygen species (ROS) scavenging capabilities and less severe cell damage, suggesting that they conferred enhanced drought tolerance in birch. This study provided an in-depth insight into the structure, evolution, expression, and function of the Dof gene family in plants.

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Identification and quantitative expression of cytokinin regulatory genes during seed and leaf development in wheat

NZGA: Research and Practice Series ◽

10.33584/rps.14.2008.3175 ◽

2010 ◽

Vol 14 ◽

pp. 131-137

Author(s):

J. Song ◽

L. Jiang ◽

P.E. Jameson

Keyword(s):

Leaf Development ◽

Flag Leaf ◽

Expression Patterns ◽

Mrna Level ◽

Gene Families ◽

Cytokinin Oxidase ◽

Isopentenyl Transferase ◽

Quantitative Expression ◽

Qrt Pcr ◽

Yield Determination

Cytokinins are intimately involved in plant growth and development and their concentration is known to change dramatically during early stages of seed development. We propose that the concentration of active cytokinin may be coordinately regulated by specific member(s) of the multi-gene families encoding biosynthesis (isopentenyl transferase, IPT), catabolism (cytokinin oxidase, CKX), and metabolism (zeatin glucosyltransferases (ZOG) and Î²-glucosidase (GLU)) genes. Our qRT-PCR data for 22 putative genes showed that the expression patterns of individual members of the Triticum aestivum (Ta)IPTs, TaCKXs, TaZOGs, and TaGLUs multi-gene families were tissue and development specific during seed and flag leaf development, with up to 90-fold changes in mRNA level. Key genes that may be involved in seed yield determination have been identified. Keywords: Wheat, flag leaf, cytokinin genes, quantitative expression, qRT-PCR

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Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

10.7287/peerj.preprints.27819v1 ◽

2019 ◽

Author(s):

Yong Zhou ◽

Yuan Cheng ◽

Chunpeng Wan ◽

Youxin Yang ◽

Jinyin Chen

Keyword(s):

Phylogenetic Analysis ◽

Gene Family ◽

Expression Patterns ◽

Future Research ◽

Biological Processes ◽

Biological Functions ◽

Specific Expression ◽

Qrt Pcr ◽

Genome Wide ◽

Intron Structure

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Genome-wide analysis of PRR gene family uncovers their roles in circadian rhythmic changes and response to drought stress in Gossypium hirsutum L.

PeerJ ◽

10.7717/peerj.9936 ◽

2020 ◽

Vol 8 ◽

pp. e9936

Author(s):

Jingjing Wang ◽

Zhaohai Du ◽

Xuehan Huo ◽

Juan Zhou ◽

Yu Chen ◽

...

Keyword(s):

Gene Expression ◽

Drought Stress ◽

Circadian Clock ◽

Gene Family ◽

Expression Patterns ◽

Enrichment Analysis ◽

Tetraploid Cotton ◽

Diurnal Changes ◽

Rhythmic Expression ◽

Qrt Pcr

Background The circadian clock not only participates in regulating various stages of plant growth, development and metabolism, but confers plant environmental adaptability to stress such as drought. Pseudo-Response Regulators (PRRs) are important component of the central oscillator (the core of circadian clock) and play a significant role in plant photoperiod pathway. However, no systematical study about this gene family has been performed in cotton. Methods PRR genes were identified in diploid and tetraploid cotton using bioinformatics methods to investigate their homology, duplication and evolution relationship. Differential gene expression, KEGG enrichment analysis and qRT-PCR were conducted to analyze PRR gene expression patterns under diurnal changes and their response to drought stress. Results A total of 44 PRR family members were identified in four Gossypium species, with 16 in G. hirsutum, 10 in G. raimondii, and nine in G. barbadense as well as in G. arboreum. Phylogenetic analysis indicated that PRR proteins were divided into five subfamilies and whole genome duplication or segmental duplication contributed to the expansion of Gossypium PRR gene family. Gene structure analysis revealed that members in the same clade are similar, and multiple cis-elements related to light and drought stress response were enriched in the promoters of GhPRR genes. qRT-PCR results showed that GhPRR genes transcripts presented four expression peaks (6 h, 9 h, 12 h, 15 h) during 24 h and form obvious rhythmic expression trend. Transcriptome data with PEG treatment, along with qRT-PCR verification suggested that members of clade III (GhPRR5a, b, d) and clade V (GhPRR3a and GhPRR3c) may be involved in drought response. This study provides an insight into understanding the function of PRR genes in circadian rhythm and in response to drought stress in cotton.

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A Role for Auxin in Triggering Lamina Outgrowth of Unifacial Leaves

Plant Physiology ◽

10.1093/plphys/kiab087 ◽

2021 ◽

Author(s):

Akira Nukazuka ◽

Takahiro Yamaguchi ◽

Hirokazu Tsukaya

Keyword(s):

Genetic Factors ◽

Auxin Transport ◽

Expression Patterns ◽

Endogenous Auxin ◽

Abaxial Side ◽

Auxin Distribution ◽

Lateral Organs ◽

Flat Shape ◽

Transport Inhibitors ◽

Unique Mechanism

Abstract A common morphological feature of typical angiosperms is the patterning of lateral organs along primary axes of asymmetry—a proximodistal, a mediolateral, and an adaxial–abaxial axis. Angiosperm leaves usually have distinct adaxial–abaxial identity, which is required for the development of a flat shape. By contrast, many unifacial leaves, consisting of only the abaxial side, show a flattened morphology. This implicates a unique mechanism that allows leaf flattening independent of adaxial–abaxial identity. In this study, we report a role for auxin in outgrowth of unifacial leaves. In two closely related unifacial-leaved species of Juncaceae, Juncus prismatocarpus with flattened leaves, and J. wallichianus with transversally radialized leaves, the auxin-responsive gene GLYCOSIDE HYDROLASE3 (GH3) displayed spatially different expression patterns within leaf primordia. Treatment of J. prismatocarpus seedlings with exogenous auxin or auxin transport inhibitors, which disturb endogenous auxin distribution, eliminated leaf flatness, resulting in a transversally radialized morphology. These treatments did not affect the radialized morphology of leaves of J. wallichianus. Moreover, elimination of leaf flatness by these treatments accompanied dysregulated expression of genetic factors needed to specify the leaf central-marginal polarity in J. prismatocarpus. The findings imply that lamina outgrowth of unifacial leaves relies on proper placement of auxin, which might induce initial leaf flattening and subsequently act to specify leaf polarity, promoting further flattening growth of leaves.

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