Analysis of PRX Gene Family and Its Function on Cell Lignification in Pears (Pyrus bretschneideri)

Class III peroxidases (PRXs) are plant-specific enzymes that play key roles in the responses to biotic and abiotic stress during plant growth and development. In addition, some peroxidases also play roles in plant lignification. In this study, a total of 114 PRX (designated PbPRXs) genes were identified in the pear (Pyrus bretschneideri Rehd) genome based on systematic analysis. These PRX genes were divided into 12 groups based on their phylogenetic relationships. We performed systematic bioinformatics analysis of the PRX genes, including analysis of gene structures, conserved motifs, phylogenetic relationships, and gene expression patterns during pear fruit growth. The PbPRXs are unevenly distributed on the 17 pear chromosomes and some of them on other scaffolds. Gene duplication event analysis indicated that whole-genome duplication (WGD) and segmental duplication play key roles in PRX gene amplification. Ka/Ks analysis suggested that most duplicated PbPRXs experienced purifying selection, with limited functional divergence during the duplication events. Furthermore, the analysis indicated that those highly expressed genes might play significant roles in the lignification of cells to form stone cells in pear fruit. We examined the expression of those highly expressed genes during fruit growth using quantitative real-time PCR (qRT-PCR), verifying differential expression patterns at different stages of fruit. This study provides useful information for further functional analysis of the PRX gene family in pears.

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A new insight into the evolution and functional divergence of FRK genes in Pyrus bretschneideri

Royal Society Open Science ◽

10.1098/rsos.171463 ◽

2018 ◽

Vol 5 (7) ◽

pp. 171463 ◽

Cited By ~ 2

Author(s):

Yunpeng Cao ◽

Shumei Li ◽

Yahui Han ◽

Dandan Meng ◽

Chunyan Jiao ◽

...

Keyword(s):

Gene Family ◽

Gene Structure ◽

Functional Divergence ◽

Sugar Content ◽

Expression Patterns ◽

Evolutionary Relationship ◽

World Market ◽

Pear Fruit ◽

Rosaceae Species ◽

Chinese White

In plants, plant fructokinases (FRKs) are considered to be the main gateway of fructose metabolism as they can phosphorylate fructose to fructose-6-phosphate. Chinese white pears ( Pyrus bretschneideri ) are one of the popular fruits in the world market; sugar content is an important factor affecting the quality of the fruit. We identified 49 FRKs from four Rosaceae species; 20 of these sequences were from Chinese white pear. Subsequently, phylogenic relationship, gene structure and micro-collinearity were analysed. Phylogenetic and exon–intron analysis classified these FRK s into 10 subfamilies, and it was aimed to further reveal the variation of the gene structure and the evolutionary relationship of this gene family. Remarkably, gene expression patterns in different tissues or different development stages of the pear fruit suggested functional redundancy for PbFRKs derived from segmental duplication or genome-wide duplication and sub-functionalization for some of them. Additionally, PbFRK11 , PbFRK13 and PbFRK16 were found to play important roles in regulating the sugar content in the fruit. Overall, this study provided important insights into the evolution of the FRK gene family in four Rosaceae species, and highlighted its roles in both pear tissue and fruits. Results presented here provide the appropriate candidate of PbFRK s that might contribute to fructose efflux in the pear fruit.

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Genome-Wide Identification and Analysis of Class III Peroxidases in Allotetraploid Cotton (Gossypium hirsutum L.) and their Responses to PK Deficiency

Genes ◽

10.3390/genes10060473 ◽

2019 ◽

Vol 10 (6) ◽

pp. 473 ◽

Cited By ~ 2

Author(s):

Duan ◽

Wang ◽

Chao ◽

Zhang ◽

Zhang

Keyword(s):

Gene Family ◽

Phylogenetic Relationships ◽

Upland Cotton ◽

Tandem Duplication ◽

Expression Profiles ◽

Expression Patterns ◽

Class Iii ◽

P Deficiency ◽

Duplication Events ◽

Class Iii Peroxidases

Class III peroxidases (PODs), commonly known as secretable class III plant peroxidases, are plant-specific enzymes that play critical roles in not only plant growth and development but also the responses to biotic and abiotic stress. In this study, we identified 198 nonredundant POD genes, designated GhPODs, with 180 PODs being predicted to secrete into apoplast. These POD genes were divided into 10 sub-groups based on their phylogenetic relationships. We performed systematic bioinformatic analysis of the POD genes, including analysis of gene structures, phylogenetic relationships, and gene expression profiles. The GhPODs are unevenly distributed on both upland cotton sub-genome A and D chromosomes. Additionally, these genes have undergone 15 segmental and 12 tandem duplication events, indicating that both segmental and tandem duplication contributed to the expansion of the POD gene family in upland cotton. Ka/Ks analysis suggested that most duplicated GhPODs experienced negative selection, with limited functional divergence during the duplication events. High-throughput RNA-seq data indicated that most highly expressed genes might play significant roles in root, stem, leaf, and fiber development. Under K or P deficiency conditions, PODs showed different expression patterns in cotton root and leaf. This study provides useful information for further functional analysis of the POD gene family in upland cotton.

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Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

BMC Ecology and Evolution ◽

10.1186/s12862-021-01873-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zhixuan Du ◽

Qitao Su ◽

Zheng Wu ◽

Zhou Huang ◽

Jianzhong Bao ◽

...

Keyword(s):

Oryza Sativa ◽

Gene Family ◽

Tandem Repeats ◽

Expression Profiles ◽

Functional Divergence ◽

Expression Patterns ◽

Regulatory Elements ◽

Genome Wide ◽

Comprehensive Information ◽

Family Gene

AbstractMultidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

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Identification, Evolutionary and Expression Analysis of PYL-PP2C-SnRK2s Gene Families in Soybean

Plants ◽

10.3390/plants9101356 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1356

Author(s):

Zhaohan Zhang ◽

Shahid Ali ◽

Tianxu Zhang ◽

Wanpeng Wang ◽

Linan Xie

Keyword(s):

Gene Family ◽

Higher Plants ◽

Expression Patterns ◽

Family Members ◽

Evolutionary Relationship ◽

Gene Families ◽

Class Iii ◽

Sequencing Data ◽

Entire Genome ◽

Core Components

Abscisic acid (ABA) plays a crucial role in various aspects of plant growth and development, including fruit development and ripening, seed dormancy, and involvement in response to various environmental stresses. In almost all higher plants, ABA signal transduction requires three core components; namely, PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs), and class III SNF-1-related protein kinase 2 (SnRK2s). The exploration of these three core components is not comprehensive in soybean. This study identified the GmPYL-PP2C-SnRK2s gene family members by using the JGI Phytozome and NCBI database. The gene family composition, conservation, gene structure, evolutionary relationship, cis-acting elements of promoter regions, and its coding protein domains were analyzed. In the entire genome of the soybean, there are 21 PYLs, 36 PP2Cs, and 21 SnRK2s genes; further, by phylogenetic and conservation analysis, 21 PYLs genes are classified into 3 groups, 36 PP2Cs genes are classified into seven groups, and 21 SnRK2s genes are classified into 3 groups. The conserved motifs and domain analysis showed that all the GmPYLs gene family members contain START-like domains, the GmPP2Cs gene family contains PP2Cc domains, and the GmSnRK2s gene family contains S_TK domains, respectively. Furthermore, based on the high-throughput transcriptome sequencing data, the results showed differences in the expression patterns of GmPYL-PP2C-SnRK2s gene families in different tissue parts of the same variety, and the same tissue part of different varieties. Our study provides a basis for further elucidation of the identification of GmPYL-PP2C-SnRK2s gene family members and analysis of their evolution and expression patterns, which helps to understand the molecular mechanism of soybean response to abiotic stress. In addition, this provides a conceptual basis for future studies of the soybean ABA core signal pathway.

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Genome-Wide Analysis of the IQM Gene Family in Rice (Oryza sativa L.)

Plants ◽

10.3390/plants10091949 ◽

2021 ◽

Vol 10 (9) ◽

pp. 1949

Author(s):

Tian Fan ◽

Tianxiao Lv ◽

Chuping Xie ◽

Yuping Zhou ◽

Changen Tian

Keyword(s):

Abiotic Stress ◽

Stress Response ◽

Gene Family ◽

Expression Profiles ◽

Expression Patterns ◽

Abiotic Stress Response ◽

Biotic And Abiotic Stress ◽

Yeast Two Hybrid ◽

Iq Motif ◽

Two Hybrid

Members of the IQM (IQ-Motif Containing) gene family are involved in plant growth and developmental processes, biotic and abiotic stress response. To systematically analyze the IQM gene family and their expression profiles under diverse biotic and abiotic stresses, we identified 8 IQM genes in the rice genome. In the current study, the whole genome identification and characterization of OsIQMs, including the gene and protein structure, genome localization, phylogenetic relationship, gene expression and yeast two-hybrid were performed. Eight IQM genes were classified into three subfamilies (I–III) according to the phylogenetic analysis. Gene structure and protein motif analyses showed that these IQM genes are relatively conserved within each subfamily of rice. The 8 OsIQM genes are distributed on seven out of the twelve chromosomes, with three IQM gene pairs involved in segmental duplication events. The evolutionary patterns analysis revealed that the IQM genes underwent a large-scale event within the last 20 to 9 million years. In addition, quantitative real-time PCR analysis of eight OsIQMs genes displayed different expression patterns at different developmental stages and in different tissues as well as showed that most IQM genes were responsive to PEG, NaCl, jasmonic acid (JA), abscisic acid (ABA) treatment, suggesting their crucial roles in biotic, and abiotic stress response. Additionally, a yeast two-hybrid assay showed that OsIQMs can interact with OsCaMs, and the IQ motif of OsIQMs is required for OsIQMs to combine with OsCaMs. Our results will be valuable to further characterize the important biological functions of rice IQM genes.

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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 Analysis of the Rice Mate Gene Family: Identification, Genomic Organization and Expression Profiles in Response to Abiotic Stresses

10.21203/rs.3.rs-62337/v1 ◽

2020 ◽

Author(s):

Zhixuan Du ◽

Qitao Su ◽

Zheng Wu ◽

Zhou Huang ◽

Jianzhong Bao ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Gene Family ◽

Abiotic Stresses ◽

Expression Profiles ◽

Functional Divergence ◽

Expression Patterns ◽

Chemical Properties ◽

Motif Analysis ◽

Functional Homology ◽

Exogenous Compounds

Abstract Background: Multidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice.Results: In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. In addition, physical and chemical properties of the encoded proteins, subcellular localization, chromosome localization, stress-related cis-elements in abiotic stresses were determined, and a phylogenetic analysis and conserved motif analysis were performed. The rice MATE family can be divided into four subfamilies. It is speculated that members of the rice MATE family have many potential functions, such as the transport and accumulation of flavonoids and alkaloids, the extrusion of plant or exogenous compounds, the regulation of disease resistance and the response to abiotic stress, based on the proteins and cis-acting elements with known functions in the same subfamily. Analysis of gene expression showed that most of the genes were constitutively expressed. Furthermore, eight MATE genes were chosen for qRT-PCR-based analysis and showed differential expression patterns in response to salt and drought stress. Conclusions: Phylogenetic analysis, element prediction, expression data and homology with other species provided strong evidence for functional homology of MATE gene in rice. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

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Identification of the GRAS gene family in the Brassica juncea genome provides insight into its role in stem swelling in stem mustard

PeerJ ◽

10.7717/peerj.6682 ◽

2019 ◽

Vol 7 ◽

pp. e6682 ◽

Cited By ~ 4

Author(s):

Mengyao Li ◽

Bo Sun ◽

Fangjie Xie ◽

Ronggao Gong ◽

Ya Luo ◽

...

Keyword(s):

Gene Family ◽

Brassica Juncea ◽

Expression Profiles ◽

Functional Divergence ◽

Expression Patterns ◽

Functional Characterization ◽

Regulatory Elements ◽

Amino Acid Properties ◽

Plant Signal Transduction ◽

Gras Gene

GRAS transcription factors are known to play important roles in plant signal transduction and development. A comprehensive study was conducted to explore the GRAS family in the Brassica juncea genome. A total of 88 GRAS genes were identified which were categorized into nine groups according to the phylogenetic analysis. Gene structure analysis showed a high group-specificity, which corroborated the gene grouping results. The chromosome distribution and sequence analysis suggested that gene duplication events are vital for the expansion of GRAS genes in the B. juncea genome. The changes in evolution rates and amino acid properties among groups might be responsible for their functional divergence. Interaction networks and cis-regulatory elements were analyzed including DELLA and eight interaction proteins (including four GID1, two SLY1, and two PIF3 proteins) that are primarily involved in light and hormone signaling. To understand their regulatory role in growth and development, the expression profiles of BjuGRASs and interaction genes were examined based on transcriptome data and qRT-PCR, and selected genes (BjuGRAS3, 5, 7, 8, 10, BjuB006276, BjuB037910, and BjuA021658) had distinct temporal expression patterns during stem swelling, indicating that they possessed diverse regulatory functions during the developmental process. These results contribute to our understanding on the GRAS gene family and provide the basis for further investigations on the evolution and functional characterization of GRAS genes.

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Differential Expression of Members of the β-Galactosidase Gene Family during Japanese Pear (Pyrus pyrifolia L.) Fruit Growth and On-tree Ripening

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.130.6.819 ◽

2005 ◽

Vol 130 (6) ◽

pp. 819-829 ◽

Cited By ~ 13

Author(s):

Akira Tateishi ◽

Kenji Nagashima ◽

Francis M. Mathooko ◽

Mercy W. Mwaniki ◽

Yasutaka Kubo ◽

...

Keyword(s):

Cell Wall ◽

Consensus Sequence ◽

Expression Patterns ◽

Fruit Growth ◽

Japanese Pear ◽

Glycoside Hydrolase Family ◽

Pyrus Pyrifolia ◽

Pear Fruit ◽

Ripe Fruit ◽

Cell Wall Disassembly

Galactosidases are thought to play a key role in cell wall metabolism during fruit growth and ripening. In this study we cloned seven β-galactosidase (β-Gal) cDNAs from japanese pear fruit and designated them PpGAL2, PpGAL3, Pp-GAL4, PpGAL5, PpGAL6, PpGAL7, and PpGAL8, in addition to the previously described JP-GAL hereinafter termed PpGAL1. mRNA expression patterns of these clones were characterized throughout fruit growth and on-tree ripening, and in leaves and shoots in three japanese pear cultivars, `Housui', `Kousui', and `Niitaka'. The shared amino acid sequence identity among the eight japanese pear β-Gal (PpGAL) clones ranged from 50% to 60%. They all contained the putative active site containing consensus sequence pattern G-G-P-[LIVM](2)-x(2)-Q-X-E-N-E-[FY] belonging to glycoside hydrolase family 35. Expression of all the clones was both development- and tissue-specific. PpGAL1 and Pp-GAL4 were only expressed in the ripe fruit while PpGAL2 and PpGAL3 were expressed in both expanding and ripening fruit with their abundance being highest in the ripe fruit. The abundance of PpGAL5, PpGAL6, and PpGAL7 mRNAs was highest in expanding fruit but decreased drastically upon the onset of ripening. PpGAL8 was only detected in very young fruit (15 days after full bloom) and not in expanding and ripening fruit. These results indicate that in japanese pear fruit β-Gal is encoded by a multigene family whose members show distinct and overlapping expression during the various phases of fruit development. Some of the members are not only fruit-specific but also ripening-specific and, therefore, may play a crucial role in cell wall disassembly during japanese pear fruit softening.

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MYB Transcription Factor Family in Sweet Cherry (Prunus avium L.): Genome-wide Investigation, Evolution, Structure, Characterization and Expression Patterns

10.21203/rs.3.rs-783177/v1 ◽

2021 ◽

Author(s):

Irfan Ali Sabir ◽

Muhammad Aamir Manzoor ◽

Iftikhar Hussain Shah ◽

Xunju Liu ◽

Muhmmad Salman Zahid ◽

...

Keyword(s):

Gene Family ◽

Sweet Cherry ◽

Prunus Avium ◽

Functional Divergence ◽

Expression Patterns ◽

Structure Characterization ◽

Myb Transcription Factor ◽

Molecular Characteristics ◽

Myb Genes ◽

Prunus Avium L

Abstract Back groundMYB Transcription factors (TFs) are most imperative and largest gene family in plants, which participate in development, metabolism, defense, differentiation and stress response. The MYB TFs has been studied in various plant species. However, comprehensive studies of MYB gene family in the sweet cherry (Prunus avium L.) are still unknown. ResultsIn the current study, a total of 69 MYB genes were investigated from sweet cherry genome and classified into 28 subfamilies (C1-C28 based on phylogenetic and structural analysis). Microcollinearity analysis revealed that dispersed duplication (DSD) and whole-genome duplication (WGD) events might play an important role in the expansion of the MYB genes family. Chromosomal localization, the synonymous (Ks) and nonsynonymous (Ka) analysis, molecular characteristics (pI, weight and length of amino acids) and subcellular localization were accomplished using several bioinformatics tools. Moreover, different subfamilies contained different cis-acting elements, conserved motifs analysis and introns-exons structures, representing functional divergence in the MYB family. Subsequently, the transcriptomic data exposed that MYB genes might play vital role in bud dormancy. Subsequently, the quantitative real-time qRT-PCR was carried out and the expression pattern indicated that MYB genes significantly expressed in floral bud as compared to flower and fruit. ConclusionOur comprehensive findings provide supportive insights into the evolutions, expansion complexity and functionality of PavMYB genes. These PavMYB genes should be further investigated as they seem to be brilliant candidates for dormancy manipulation in sweet cherry.

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