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

Genes ◽  
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.

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

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Tianyu Zhou ◽  
Xiping Yan ◽  
Guosong Wang ◽  
Hehe Liu ◽  
Xiang Gan ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Hormone Receptors ◽  
Expression Patterns ◽  
Family Members ◽  
Duplication Event ◽  
Promoter Regions ◽  
Evolutionary Pattern ◽  
Duplication Events ◽  
Differential Transcription

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.

Two gene duplication events in the human and primate dopamine D5 receptor gene family

Gene ◽  
1995 ◽  
Vol 154 (2) ◽  
pp. 153-158 ◽  
Author(s):  
Adriano Marchese ◽  
Timothy V. Beischlag ◽  
Tuan Nguyen ◽  
Hyman B. Niznik ◽  
Richard L. Weinshank ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Receptor Gene ◽  
Duplication Events ◽  
Dopamine D5 Receptor ◽  
Receptor Gene Family

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

2013 ◽  
Vol 40 (4) ◽  
pp. 369 ◽  
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.

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

Genome ◽  
2002 ◽  
Vol 45 (4) ◽  
pp. 693-701 ◽  
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 35–98% 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.

scholarly journals The Chalcone Isomerase Family in Cotton: Whole-Genome Bioinformatic and Expression Analyses of the Gossypium barbadense L. Response to Fusarium Wilt Infection

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1006 ◽  
Author(s):  
Qian-Li Zu ◽  
Yan-Ying Qu ◽  
Zhi-Yong Ni ◽  
Kai Zheng ◽  
Qin Chen ◽  
...  
Keyword(s):  
Gene Family ◽  
Fusarium Wilt ◽  
Pairwise Comparison ◽  
Gossypium Barbadense ◽  
Chalcone Isomerase ◽  
Whole Genome ◽  
Systematic Analysis ◽  
Preliminary Model ◽  
Cotton Species ◽  
Duplication Events

Chalcone isomerase (CHI) is a key component of phenylalanine metabolism that can produce a variety of flavonoids. However, little information and no systematic analysis of CHI genes is available for cotton. Here, we identified 33 CHI genes in the complete genome sequences of four cotton species (Gossypium arboretum L., Gossypium raimondii L., Gossypium hirsutum L., and Gossypium barbadense L.). Cotton CHI proteins were classified into two main groups, and whole-genome/segmental and dispersed duplication events were important in CHI gene family expansion. qRT-PCR and semiquantitative RT-PCR results suggest that CHI genes exhibit temporal and spatial variation and respond to infection with Fusarium wilt race 7. A preliminary model of CHI gene involvement in cotton evolution was established. Pairwise comparison revealed that seven CHI genes showed higher expression in cultivar 06-146 than in cultivar Xinhai 14. Overall, this whole-genome identification unlocks a new approach to the comprehensive functional analysis of the CHI gene family, which may be involved in adaptation to plant pathogen stress.

scholarly journals Expansion and Molecular Characterization of AP2/ERF Gene Family in Wheat (Triticum aestivum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Muhammad Waheed Riaz ◽  
Jie Lu ◽  
Liaqat Shah ◽  
Liu Yang ◽  
Can Chen ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Triticum Aestivum L ◽  
Vital Role ◽  
Systematic Analysis ◽  
Wheat Seedlings ◽  
A Genome ◽  
Duplication Events

The AP2/ERF is a large protein family of transcription factors, playing an important role in signal transduction, plant growth, development, and response to various stresses. AP2/ERF super-family is identified and functionalized in a different plant but no comprehensive and systematic analysis in wheat (Triticum aestivum L.) has been reported. However, a genome-wide and functional analysis was performed and identified 322 TaAP2/ERF putative genes from the wheat genome. According to the phylogenetic and structural analysis, TaAP2/ERF genes were divided into 12 subfamilies (Ia, Ib, Ic, IIa, IIb, IIc, IIIa, IIIb, IIIc, IVa, IVb, and IVc). Furthermore, conserved motifs and introns/exons analysis revealed may lead to functional divergence within clades. Cis-Acting analysis indicated that many elements were involved in stress-related and plant development. Chromosomal location showed that 320 AP2/ERF genes were distributed among 21 chromosomes and 2 genes were present in a scaffold. Interspecies microsynteny analysis revealed that maximum orthologous between Arabidopsis, rice followed by wheat. Segment duplication events have contributed to the expansion of the AP2/ERF family and made this family larger than rice and Arabidopsis. Additionally, AP2/ERF genes were differentially expressed in wheat seedlings under the stress treatments of heat, salt, and drought, and expression profiles were verified by qRT-PCR. Remarkably, the RNA-seq data exposed that AP2/ERF gene family might play a vital role in stress-related. Taken together, our findings provided useful and helpful information to understand the molecular mechanism and evolution of the AP2/ERF gene family in wheat.

scholarly journals Dialog between Kingdoms: Enemies, Allies and Peptide Phytohormones

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2243
Author(s):  
Irina Dodueva ◽  
Maria Lebedeva ◽  
Lyudmila Lutova
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Plant Immunity ◽  
Peptide Hormones ◽  
Parasitic Nematodes ◽  
Plant Parasitic Nematodes ◽  
Plant Body ◽  
Genes Encoding ◽  
Environmental Responses ◽  
Bacteria And Fungi

Various plant hormones can integrate developmental and environmental responses, acting in a complex network, which allows plants to adjust their developmental processes to changing environments. In particular, plant peptide hormones regulate various aspects of plant growth and development as well as the response to environmental stress and the interaction of plants with their pathogens and symbionts. Various plant-interacting organisms, e.g., bacterial and fungal pathogens, plant-parasitic nematodes, as well as symbiotic and plant-beneficial bacteria and fungi, are able to manipulate phytohormonal level and/or signaling in the host plant in order to overcome plant immunity and to create the habitat and food source inside the plant body. The most striking example of such phytohormonal mimicry is the ability of certain plant pathogens and symbionts to produce peptide phytohormones of different classes. To date, in the genomes of plant-interacting bacteria, fungi, and nematodes, the genes encoding effectors which mimic seven classes of peptide phytohormones have been found. For some of these effectors, the interaction with plant receptors for peptide hormones and the effect on plant development and defense have been demonstrated. In this review, we focus on the currently described classes of peptide phytohormones found among the representatives of other kingdoms, as well as mechanisms of their action and possible evolutional origin.

scholarly journals Deep Evaluation to the Evolution History of Heat Shock Factor (HSF) Gene Family and Its Expansion Pattern in Seed Plants

2020 ◽  
Author(s):  
Yiying Liao ◽  
Zhiming Liu ◽  
Andrew W. Gichira ◽  
Min Yang ◽  
Ruth Wambui Mbichi ◽  
...  
Keyword(s):  
Heat Shock ◽  
Gene Duplication ◽  
Gene Family ◽  
Phylogenetic Reconstruction ◽  
Heat Shock Factor ◽  
Specific Gene ◽  
Ancestral State ◽  
Duplication Events ◽  
History Of ◽  
Lineage Specific Gene

Abstract BackgroundHSF (Heat shock factor) genes are essential in the irreplaceable functions in some of the basic developmental pathways in plants. Despite the extensive studies on the structure, function diversification, and evolution of HSF, their divergent history and gene duplication pattern remain unsolved. To further illustrate the probable divergent patterns in these subfamilies, we visited the evolutionary history of the HSF via phylogenetic reconstruction and genomic syntenic analyses by taking advantage of the increased sampling of genomic data for pteridophyta, gymnosperms and basal angiosperms. ResultsWe identified a novel clade including HSFA2, HSFA6, HSFA7, HSFA9 with complex relationship, very likely due to orthologous or paralogous genes retained after frequent gene duplication events. We suggested that HSFA9 was derived from HSFA2 through gene duplication in eudicots at ancestral state, and then expanded in a lineage-specific way. Our findings indicated that HSFB3 and HSFB5 emerged before the divergence of ancestral angiosperms, but were lost in common ancestors of monocots. We also presumed that HSFC2 was derived from HSFC1 in ancestral monocots. ConclusionThis work proposes that in the era of early differentiation of angiosperms during the radiation of flowering plants, the member size of HSF gene family was also being adjusted, accompanied with considerable sub- or neo-functionalization. The independent evolution of HSFs in eudicots and monocots, including lineage-specific gene duplication gave rise to a new gene in ancestral eudicots and monocots, and lineage-specific gene loss in ancestral monocots. Our analyses provide essential insights for studying evolution history of multigene family.

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