Evolutionary Pattern and Regulation Analysis to Support Why Diversity Functions Existed within PPAR Gene Family Members

Peroxisome proliferators-activated receptor (PPAR) gene family members exhibit distinct patterns of distribution in tissues and differ in functions. The purpose of this study is to investigate the evolutionary impacts on diversity functions of PPAR members and the regulatory differences on gene expression patterns. 63 homology sequences of PPAR genes from 31 species were collected and analyzed. The results showed that three isolated types of PPAR gene family may emerge from twice times of gene duplication events. The conserved domains of HOLI (ligand binding domain of hormone receptors) domain and ZnF_C4 (C4 zinc finger in nuclear in hormone receptors) are essential for keeping basic roles of PPAR gene family, and the variant domains of LCRs may be responsible for their divergence in functions. The positive selection sites in HOLI domain are benefit for PPARs to evolve towards diversity functions. The evolutionary variants in the promoter regions and 3′ UTR regions of PPARs result into differential transcription factors and miRNAs involved in regulating PPAR members, which may eventually affect their expressions and tissues distributions. These results indicate that gene duplication event, selection pressure on HOLI domain, and the variants on promoter and 3′ UTR are essential for PPARs evolution and diversity functions acquired.

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Identification and genes expression analysis of ATP-dependent phosphofructokinase family members among three Saccharum species

Functional Plant Biology ◽

10.1071/fp12182 ◽

2013 ◽

Vol 40 (4) ◽

pp. 369 ◽

Cited By ~ 6

Author(s):

Lin Zhu ◽

Jisen Zhang ◽

Youqiang Chen ◽

Hongyu Pan ◽

Ray Ming

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Family Members ◽

Sucrose Metabolism ◽

Expression Level ◽

Group Iii ◽

Saccharum Species ◽

Subgroup Ii ◽

Unrooted Phylogenetic Tree ◽

Duplication Events

Sugarcane contributes ~80% of sugar production in the world and is an established biofuel crop. In working towards understanding the molecular basis of high sucrose accumulation, we have annotated and analysed the ATP-dependent phosphofructokinase (PFK) gene family that catalyses the phosphorylation of D-fructose 6-phosphate to D-fructose 1,6-bisphosphate. PFKs play an essential role in sucrose metabolism in plants and their expression patterns are unknown in sugarcane. In this study, based on the sorghum genome and sugarcane EST database, 10 PFK gene members were annotated and further verified by PCR using sugarcane genomic DNA. An unrooted phylogenetic tree was constructed with the deduced protein sequences of PFKs that were from the assembly of cDNA library of sugarcane and other plants. The results showed that gene duplication events and the retention rate after genome wide or segmental duplications occurred in higher frequency in monocots than in dicots and the genes in subgroup II of group III were likely originated from recent duplication events. Quantitative RT–PCR was performed to investigate the gene expression of 10 PFK genes in five tissues of three Saccharum species, including two developmental stages in leaves and three in culms. Of the PFK family members in sugarcane, ScPFK6, 7 and 8 appeared to be the primary isoforms based on the highly abundant expression of these three genes. ScPFK7 showed high expression level in the leaves, suggesting a potential role in sucrose metabolism. ScPFK8 had lower expression level in Saccharum officinarum L. than in the other two species, suggesting negative regulation of sucrose metabolism, which might have contributed to the high sugar content of S. officinarum. The genes in monocot specific subgroup II of group III, PFK7, 8 and 9, showed variation among the three Saccharum species, suggesting potential functional redundancy. Our results provide detailed annotation and analysis of the PFK gene family in sugarcane. Further elucidation of the role of ScPFK8 in the domestication process of sugarcane would be useful.

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Identification, structure, and differential expression of members of a BURP domain containing protein family in soybean

Genome ◽

10.1139/g02-032 ◽

2002 ◽

Vol 45 (4) ◽

pp. 693-701 ◽

Cited By ~ 30

Author(s):

Cheryl Granger ◽

Virginia Coryell ◽

Anupama Khanna ◽

Paul Keim ◽

Lila Vodkin ◽

...

Keyword(s):

Glycine Max ◽

Gene Duplication ◽

Expressed Sequence Tag ◽

Signal Sequence ◽

Expression Patterns ◽

Family Members ◽

Specific Expression ◽

Burp Domain ◽

Duplication Events ◽

Expressed Sequence

Expressed sequence tags (ESTs) exhibiting homology to a BURP domain containing gene family were identified from the Glycine max (L.) Merr. EST database. These ESTs were assembled into 16 contigs of variable sizes and lengths. Consistent with the structure of known BURP domain containing proteins, the translation products exhibit a modular structure consisting of a C-terminal BURP domain, an N-terminal signal sequence, and a variable internal region. The soybean family members exhibit 3598% similarity in a ~100-amino-acid C-terminal region, and a phylogenetic tree constructed using this region shows that some soybean family members group together in closely related pairs, triplets, and quartets, whereas others remain as singletons. The structure of these groups suggests that multiple gene duplication events occurred during the evolutionary history of this family. The depth and diversity of G. max EST libraries allowed tissue-specific expression patterns of the putative soybean BURPs to be examined. Consistent with known BURP proteins, the newly identified soybean BURPs have diverse expression patterns. Furthermore, putative paralogs can have both spatially and quantitatively distinct expression patterns. We discuss the functional and evolutionary implications of these findings, as well as the utility of EST-based analyses for identifying and characterizing gene families.Key words: BURP domain, expressed sequence tag, gene duplication, Glycine max.

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Genome-Wide Analysis of LysM-Containing Gene Family in Wheat: Structural and Phylogenetic Analysis during Development and Defense

Genes ◽

10.3390/genes12010031 ◽

2020 ◽

Vol 12 (1) ◽

pp. 31

Author(s):

Zheng Chen ◽

Zijie Shen ◽

Da Zhao ◽

Lei Xu ◽

Lijun Zhang ◽

...

Keyword(s):

Gene Duplication ◽

Gene Family ◽

Plant Pathogens ◽

Plant Immunity ◽

Family Members ◽

Distribution Analysis ◽

Systematic Analysis ◽

Defense Proteins ◽

Duplication Events ◽

Bacteria And Fungi

The lysin motif (LysM) family comprise a number of defense proteins that play important roles in plant immunity. The LysM family includes LysM-containing receptor-like proteins (LYP) and LysM-containing receptor-like kinase (LYK). LysM generally recognizes the chitin and peptidoglycan derived from bacteria and fungi. Approximately 4000 proteins with the lysin motif (Pfam PF01476) are found in prokaryotes and eukaryotes. Our study identified 57 LysM genes and 60 LysM proteins in wheat and renamed these genes and proteins based on chromosome distribution. According to the phylogenetic and gene structure of intron–exon distribution analysis, the 60 LysM proteins were classified into seven groups. Gene duplication events had occurred among the LysM family members during the evolution process, resulting in an increase in the LysM gene family. Synteny analysis suggested the characteristics of evolution of the LysM family in wheat and other species. Systematic analysis of these species provided a foundation of LysM genes in crop defense. A comprehensive analysis of the expression and cis-elements of LysM gene family members suggested that they play an essential role in defending against plant pathogens. The present study provides an overview of the LysM family in the wheat genome as well as information on systematic, phylogenetic, gene duplication, and intron–exon distribution analyses that will be helpful for future functional analysis of this important protein family, especially in Gramineae species.

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Catalase (CAT) Gene Family in Wheat (Triticum aestivum L.): Evolution, Expression Pattern and Function Analysis

International Journal of Molecular Sciences ◽

10.3390/ijms23010542 ◽

2022 ◽

Vol 23 (1) ◽

pp. 542

Author(s):

Yan Zhang ◽

Lanjie Zheng ◽

Liu Yun ◽

Li Ji ◽

Guanhui Li ◽

...

Keyword(s):

Gene Family ◽

Function Analysis ◽

Expression Patterns ◽

Triticum Aestivum L ◽

Duplication Event ◽

Oxygen Deficit ◽

Promoter Regions ◽

Relationship Analysis ◽

Living Organisms ◽

Almost All

Catalases (CATs) are present in almost all living organisms and play important roles in plant development and response to various stresses. However, there is relatively little information on CAT genes in wheat and related Triticeae species. A few studies on CAT family genes in wheat have been reported. In this study, ten CAT proteins (TaCATs) were identified in wheat and classified into three groups based on their phylogenetic features and sequence analysis. The analysis of the structure and motif composition of the TaCAT proteins suggested that a segmental duplication event occurred in the TaCAT gene family. Collinearity relationship analysis among different species showed that there were three orthologous CAT genes in rice and in maize. By analyzing the cis-elements in the promoter regions, we speculated that TaCAT genes expression might be regulated by light, oxygen deficit, methyl jasmonate and abscisic acid, and by transcription factors such as MYB. A Gene Ontology (GO)-based analysis showed that TaCAT proteins may be related to the response to various stresses, are cytoplasm localized, and may function as antioxidant enzymes. RT-qPCR and transcriptome data analyses exhibited distinct expression patterns of TaCAT genes in different tissues and in response to various treatments. In this study, a comprehensive analysis of wheat CAT genes was performed, enriching our knowledge of CAT genes and providing a foundation for further functional analyses of this gene family in wheat.

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Identification of members of the P-glycoprotein multigene family.

Molecular and Cellular Biology ◽

10.1128/mcb.9.3.1224 ◽

1989 ◽

Vol 9 (3) ◽

pp. 1224-1232 ◽

Cited By ~ 146

Author(s):

W F Ng ◽

F Sarangi ◽

R L Zastawny ◽

L Veinot-Drebot ◽

V Ling

Keyword(s):

Multidrug Resistance ◽

Gene Duplication ◽

Gene Family ◽

Multigene Family ◽

Rhesus Monkeys ◽

Genomic Library ◽

Duplication Event ◽

Glycoprotein Gene ◽

P Glycoprotein ◽

Exon Probe

Overproduction of P-glycoprotein is intimately associated with multidrug resistance. This protein appears to be encoded by a multigene family. Thus, differential expression of different members of this family may contribute to the complexity of the multidrug resistance phenotype. Three lambda genomic clones isolated from a hamster genomic library represent different members of the hamster P-glycoprotein gene family. Using a highly conserved exon probe, we found that the hamster P-glycoprotein gene family consists of three genes. We also found that the P-glycoprotein gene family consists of three genes in mice but has only two genes in humans and rhesus monkeys. The hamster P-glycoprotein genes have similar exon-intron organizations within the 3' region encoding the cytoplasmic domains. We propose that the hamster P-glycoprotein gene family arose from gene duplication. The hamster pgp1 and pgp2 genes appear to be more closely related to each other than either gene is to the pgp3 gene. We speculate that the hamster pgp1 and pgp2 genes arose from a recent gene duplication event and that primates did not undergo this duplication and therefore contain only two P-glycoprotein genes.

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Unique and Overlapping Expression Patterns among the Arabidopsis 1-Amino-Cyclopropane-1-Carboxylate Synthase Gene Family Members

PLANT PHYSIOLOGY ◽

10.1104/pp.104.049999 ◽

2004 ◽

Vol 136 (2) ◽

pp. 2982-3000 ◽

Cited By ~ 236

Author(s):

Atsunari Tsuchisaka ◽

Athanasios Theologis

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Family Members

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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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Comprehensive Analysis of the Chitinase Gene Family in Cucumber (Cucumis sativus L.): From Gene Identification and Evolution to Expression in Response to Fusarium oxysporum

International Journal of Molecular Sciences ◽

10.3390/ijms20215309 ◽

2019 ◽

Vol 20 (21) ◽

pp. 5309 ◽

Cited By ~ 2

Author(s):

Ezra S. Bartholomew ◽

Kezia Black ◽

Zhongxuan Feng ◽

Wan Liu ◽

Nan Shan ◽

...

Keyword(s):

Gene Family ◽

Fusarium Oxysporum ◽

Expression Patterns ◽

Chitinase Gene ◽

Cucumis Sativus L ◽

Binding Domains ◽

Organ Specific ◽

Duplication Events ◽

Chitinase Genes ◽

Related Proteins

Chitinases, a subgroup of pathogenesis-related proteins, are responsible for catalyzing the hydrolysis of chitin. Accumulating reports indicate that chitinases play a key role in plant defense against chitin-containing pathogens and are therefore good targets for defense response studies. Here, we undertook an integrated bioinformatic and expression analysis of the cucumber chitinases gene family to identify its role in defense against Fusarium oxysporum f. sp. cucumerinum. A total of 28 putative chitinase genes were identified in the cucumber genome and classified into five classes based on their conserved catalytic and binding domains. The expansion of the chitinase gene family was due mainly to tandem duplication events. The expression pattern of chitinase genes was organ-specific and 14 genes were differentially expressed in response to F. oxysporum challenge of fusarium wilt-susceptible and resistant lines. Furthermore, a class I chitinase, CsChi23, was constitutively expressed at high levels in the resistant line and may play a crucial role in building a basal defense and activating a rapid immune response against F. oxysporum. Whole-genome re-sequencing of both lines provided clues for the diverse expression patterns observed. Collectively, these results provide useful genetic resource and offer insights into the role of chitinases in cucumber-F. oxysporum interaction.

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