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

2018 ◽  
Vol 5 (7) ◽  
pp. 171463 ◽  
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.

scholarly journals New insights into the evolution and functional divergence of the CIPK gene family in Saccharum

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Weihua Su ◽  
Yongjuan Ren ◽  
Dongjiao Wang ◽  
Long Huang ◽  
Xueqin Fu ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Structure ◽  
Quantitative Polymerase Chain Reaction ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Functional Study ◽  
Last Common Ancestor ◽  
Duplicated Genes ◽  
Duplication Events

Abstract Background Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) are the primary components of calcium sensors, and play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to exogenous stresses. Results In this study, 48 CIPK genes (SsCIPKs) were identified from the genome of Saccharum spontaneum. Phylogenetic reconstruction suggested that the SsCIPK gene family may have undergone six gene duplication events from the last common ancestor (LCA) of SsCIPKs. Whole-genome duplications (WGDs) served as the driving force for the amplification of SsCIPKs. The Nonsynonymous to synonymous substitution ratio (Ka/Ks) analysis showed that the duplicated genes were possibly under strong purifying selection pressure. The divergence time of these duplicated genes had an average duplication time of approximately 35.66 Mya, suggesting that these duplication events occurred after the divergence of the monocots and eudicots (165 Mya). The evolution of gene structure analysis showed that the SsCIPK family genes may involve intron losses. Ten ScCIPK genes were amplified from sugarcane (Saccharum spp. hybrids). The results of real-time quantitative polymerase chain reaction (qRT-PCR) demonstrated that these ten ScCIPK genes had different expression patterns under abscisic acid (ABA), polyethylene glycol (PEG), and sodium chloride (NaCl) stresses. Prokaryotic expression implied that the recombinant proteins of ScCIPK3, − 15 and − 17 could only slightly enhance growth under salinity stress conditions, but the ScCIPK21 did not. Transient N. benthamiana plants overexpressing ScCIPKs demonstrated that the ScCIPK genes were involved in responding to external stressors through the ethylene synthesis pathway as well as to bacterial infections. Conclusions In generally, a comprehensive genome-wide analysis of evolutionary relationship, gene structure, motif composition, and gene duplications of SsCIPK family genes were performed in S. spontaneum. The functional study of expression patterns in sugarcane and allogenic expressions in E. coli and N. benthamiana showed that ScCIPKs played various roles in response to different stresses. Thus, these results improve our understanding of the evolution of the CIPK gene family in sugarcane as well as provide a basis for in-depth functional studies of CIPK genes in sugarcane.

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

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1874
Author(s):  
Zhihua Xie ◽  
Weikang Rui ◽  
Yazhou Yuan ◽  
Xiaofei Song ◽  
Xing Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Phylogenetic Relationships ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Fruit Growth ◽  
Event Analysis ◽  
Class Iii ◽  
Biotic And Abiotic Stress ◽  
Pear Fruit ◽  
Highly Expressed Genes

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.

scholarly journals Genome-Wide Identification and Characterization of Polygalacturonase Gene Family in Maize (Zea mays L.)

2021 ◽  
Vol 22 (19) ◽  
pp. 10722
Author(s):  
Lu Lu ◽  
Quancan Hou ◽  
Linlin Wang ◽  
Tianye Zhang ◽  
Wei Zhao ◽  
...  
Keyword(s):  
Zea Mays ◽  
Gene Family ◽  
Zea Mays L ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Evolutionary Relationship ◽  
Segmental Duplications

Polygalacturonase (PG, EC 3.2.1.15) is a crucial enzyme for pectin degradation and is involved in various developmental processes such as fruit ripening, pollen development, cell expansion, and organ abscission. However, information on the PG gene family in the maize (Zea mays L.) genome and the specific members involved in maize anther development are still lacking. In this study, we identified 55 PG family genes from the maize genome and further characterized their evolutionary relationship and expression patterns. Phylogenetic analysis revealed that ZmPGs are grouped into six Clades, and gene structures of the same Clade are highly conserved, suggesting their functional conservation. The ZmPGs are randomly distributed across maize chromosomes, and collinearity analysis showed that many ZmPGs might be derived from tandem duplications and segmental duplications, and these genes are under purifying selection. Furthermore, gene expression analysis provided insights into possible functional divergence among ZmPGs. Based on the RNA-seq data analysis, we found that many ZmPGs are expressed in various tissues while 18 ZmPGs are highly expressed in maize anther, and their detailed expression profiles in different anther developmental stages were further investigated by using RT-qPCR analysis. These results provide valuable information for further functional characterization and application of the ZmPGs in maize.

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

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.

scholarly journals Genome-wide identification and comparative analysis of the ADH gene family in Chinese white pear (Pyrus bretschneideri) and other Rosaceae species

Genomics ◽  
2020 ◽  
Vol 112 (5) ◽  
pp. 3484-3496
Author(s):  
Weiwei Zeng ◽  
Xin Qiao ◽  
Qionghou Li ◽  
Chunxin Liu ◽  
Jun Wu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Gene Family ◽  
Rosaceae Species ◽  
Chinese White ◽  
Genome Wide ◽  
Adh Gene

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

Plants ◽  
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.

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

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.

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 Integrative Analysis of the Core Fruit Lignification Toolbox in Pear Reveals Targets for Fruit Quality Bioengineering

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 504 ◽  
Author(s):  
Yunpeng Cao ◽  
Xiaoxu Li ◽  
Lan Jiang
Keyword(s):  
Fruit Quality ◽  
Expression Patterns ◽  
Lignin Biosynthesis ◽  
Integrative Analysis ◽  
Bimolecular Fluorescence Complementation ◽  
Pear Fruit ◽  
Cell Content ◽  
Tandem Gene Duplication ◽  
Stone Cell ◽  
Chinese White

Stone cell content is an important factor affecting pear fruit flavor. Lignin, a major component of pear stone cells, hinders the quality and value of commercial fruit. The completion of the Chinese white pear (Pyrus bretschneideri) genome sequence provides an opportunity to perform integrative analysis of the genes encoding the eleven protein families (i.e., PAL, C4H, 4CL, HCT, C3H, CSE, CCoAOMT, CCR, F5H, COMT, and CAD) in the phenylpropanoid pathway. Here, a systematic study based on expression patterns and phylogenetic analyses was performed to identify the members of each gene family potentially involved in the lignification in the Chinese white pear. The phylogenetic analysis suggested that 35 P. bretschneideri genes belong to bona fide lignification clade members. Compared to other plants, some multigene families are expanded by tandem gene duplication, such as HCT, C3H, COMT, and CCR. RNA sequencing was used to study the expression patterns of the genes in different tissues, including leaf, petal, bud, sepal, ovary, stem, and fruit. Eighteen genes presented a high expression in fruit, indicating that these genes may be involved in the biosynthesis of lignin in pear fruit. Similarly to what has been observed for Populus trichocarpa, a bimolecular fluorescence complementation (BiFC) experiment indicated that P. bretschneideri C3H and C4H might also interact with each other to regulate monolignol biosynthesis in P. bretschneideri, ultimately affecting the stone cell content in pear fruits. The identification of the major genes involved in lignin biosynthesis in pear fruits provides the basis for the development of strategies to improve fruit quality.

scholarly journals A genome-wide identification of the BLH gene family reveals BLH1 involved in cotton fiber development

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Cuixia LIU ◽  
Zhifang LI ◽  
Lingling DOU ◽  
Yi YUAN ◽  
Changsong ZOU ◽  
...  
Keyword(s):  
Gibberellic Acid ◽  
Gene Family ◽  
Gene Structure ◽  
Natural Fiber ◽  
Chromosomal Location ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Fiber Development ◽  
Expression Levels ◽  
A Genome

Abstract Background Cotton is the world’s largest and most important source of renewable natural fiber. BEL1-like homeodomain (BLH) genes are ubiquitous in plants and have been reported to contribute to plant development. However, there is no comprehensive characterization of this gene family in cotton. In this study, 32, 16, and 18 BLH genes were identified from the G. hirsutum, G. arboreum, and G. raimondii genome, respectively. In addition, we also studied the phylogenetic relationships, chromosomal location, gene structure, and gene expression patterns of the BLH genes. Results The results indicated that these BLH proteins were divided into seven distinct groups by phylogenetic analysis. Among them, 25 members were assigned to 15 chromosomes. Furthermore, gene structure, chromosomal location, conserved motifs, and expression level of BLH genes were investigated in G. hirsutum. Expression profiles analysis showed that four genes (GhBLH1_3, GhBLH1_4, GhBLH1_5, and GhBLH1_6) from BLH1 subfamily were highly expressed during the fiber cell elongation period. The expression levels of these genes were significantly induced by gibberellic acid and brassinosteroid, but not auxin. Exogenous application of gibberellic acid significantly enhanced GhBLH1_3, GhBLH1_4, and GhBLH1_5 transcripts. Expression levels of GhBLH1_3 and GhBLH1_4 genes were significantly increased under brassinosteroid treatment. Conclusions The BLH gene family plays a very important role in many biological processes during plant growth and development. This study deepens our understanding of the role of the GhBLH1 gene involved in fiber development and will help us in breeding better cotton varieties in the future.

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