scholarly journals Identification and Characterization of Wall-Associated Kinase (WAK) and WAK-like (WAKL) Gene Family in Juglans regia and Its Wild Related Species Juglans mandshurica

Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 134
Author(s):  
Mengdi Li ◽  
Jiayu Ma ◽  
Hengzhao Liu ◽  
Mengwei Ou ◽  
Hang Ye ◽  
...  
Keyword(s):  
Gene Family ◽  
Related Species ◽  
Juglans Regia ◽  
Critical Role ◽  
Gene Expression Pattern ◽  
Gene Families ◽  
Plant Response ◽  
Potential Candidate ◽  
Evolutionary Analysis ◽  
Juglans Mandshurica

Wall-associated kinase (WAK) and WAK-like kinase (WAKL) are receptor-like kinases (RLKs), which play important roles in signal transduction between the cell wall and the cytoplasm in plants. WAK/WAKLs have been studied in many plants, but were rarely studied in the important economic walnut tree. In this study, 27 and 14 WAK/WAKL genes were identified in Juglans regia and its wild related species Juglans mandshurica, respectively. We found tandem duplication might play a critical role in the expansion of WAK/WAKL gene family in J. regia, and most of the WAK/WAKL homologous pairs underwent purified selection during evolution. All WAK/WAKL proteins have the extracellular WAK domain and the cytoplasmic protein kinase domain, and the latter was more conserved than the former. Cis-acting elements analysis showed that WAK/WAKL might be involved in plant growth and development, plant response to abiotic stress and hormones. Gene expression pattern analysis further indicated that most WAK/WAKL genes in J. regia might play a role in the development of leaves and be involved in plant response to biotic stress. Our study provides a new perspective for the evolutionary analysis of gene families in tree species and also provides potential candidate genes for studying WAK/WAKL gene function in walnuts.

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.

Genome-wide identification and expression analysis of SnRK2 gene family in mungbean (Vigna radiata) in response to drought stress

2020 ◽  
Vol 71 (5) ◽  
pp. 469
Author(s):  
Annaira Fatima ◽  
Muhammad Jadoon Khan ◽  
Hassaan Mehboob Awan ◽  
Malik Nadeem Akhtar ◽  
Nazia Bibi ◽  
...  
Keyword(s):  
Drought Stress ◽  
Gene Family ◽  
Real Time ◽  
Vigna Radiata ◽  
Crop Production ◽  
Gene Prediction ◽  
Critical Role ◽  
Evolutionary Analysis ◽  
Genome Wide Analysis ◽  
Genome Wide

Drought stress causes lower crop production globally. Plants have acquired many adaptations to overcome drought stress. Mungbean (Vigna radiata (L.) R.Wilczek) is a legume crop widely cultivated in South, East and Southeast Asia. It is grown in high-temperature areas where drought is the main cause of reduced plant growth and productivity. Plants cope with drought stress by activating different signalling mechanisms. The sucrose non-fermenting-1-related protein kinase 2 family (SnRK2s) is known to play vital roles in osmotic stress and in abscisic acid (ABA) signalling pathways by phosphorylating downstream targets. The genes encoding SnRK2s in mungbean and their detailed characterisation remain unexplored. We have conducted extensive genome-wide analysis for gene prediction, in silico gene analysis, evolutionary analysis and gene-expression profiling under drought-stress conditions by quantitative real-time PCR. Through genome-wide analysis, eight SnRK2 genes were predicted in the mungbean genome and were assigned the names VrSnRK2.1–VrSnRK2.8, according to their order on the chromosomes. The VrSnRK2 genes identified were classified into three clusters based on their phylogenetic relationship with those of Arabidopsis thaliana. Drought stress was imposed on 11-day-old mungbean plants by completely withholding water for 3 days. According to real-time qPCR data, the expression of most of the VrSnRK2 genes was induced by drought stress, indicating their role in the drought-stress response. One of the genes, namely SnRK2.6c, showed highest expression level (12-fold) under drought stress, possibly indicating a critical role under water-deficit conditions. These data provide important information about the VrSnRK2 gene family in mungbean. The results will help in future functional characterisation of VrSnRK2 genes.

scholarly journals Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study

2020 ◽  
Vol 12 (3) ◽  
pp. 185-202
Author(s):  
Xia Han ◽  
Jindan Guo ◽  
Erli Pang ◽  
Hongtao Song ◽  
Kui Lin
Keyword(s):  
Gene Family ◽  
De Novo ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Genome Phylogeny ◽  
Partial Homology

Abstract How have genes evolved within a well-known genome phylogeny? Many protein-coding genes should have evolved as a whole at the gene level, and some should have evolved partly through fragments at the subgene level. To comprehensively explore such complex homologous relationships and better understand gene family evolution, here, with de novo-identified modules, the subgene units which could consecutively cover proteins within a set of closely related species, we applied a new phylogeny-based approach that considers evolutionary models with partial homology to classify all protein-coding genes in nine Drosophila genomes. Compared with two other popular methods for gene family construction, our approach improved practical gene family classifications with a more reasonable view of homology and provided a much more complete landscape of gene family evolution at the gene and subgene levels. In the case study, we found that most expanded gene families might have evolved mainly through module rearrangements rather than gene duplications and mainly generated single-module genes through partial gene duplication, suggesting that there might be pervasive subgene rearrangement in the evolution of protein-coding gene families. The use of a phylogeny-based approach with partial homology to classify and analyze protein-coding gene families may provide us with a more comprehensive landscape depicting how genes evolve within a well-known genome phylogeny.

scholarly journals Genome-Wide Identification and Transcriptional Expression Profiles of the F-box Gene Family in Common Walnut (Juglans regia L.)

Forests ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 275 ◽  
Author(s):  
Feng Yan ◽  
Huijuan Zhou ◽  
Ming Yue ◽  
Ge Yang ◽  
Huaizhu Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Development ◽  
Juglans Regia ◽  
Critical Role ◽  
Transcriptional Expression ◽  
Genome Wide ◽  
A Genome ◽  
Male Flowers ◽  
Common Walnut ◽  
Female Flowers

The common walnut (or Persian walnut), Juglans regia L., is an economically important temperate tree species valued for both its edible nut and high-quality wood. F-box gene family members are involved in plant development, which includes regulating plant development, reproduction, cellular protein degradation, response to biotic and abiotic stresses, and flowering. However, in common walnut (J. regia), there are no reports about the F-box gene family. Here, we report a genome-wide identification of J. regia F-box genes and analyze their phylogeny, duplication, microRNA, pathway, and transcriptional expression profile. In this study, 74 F-box genes were identified and clustered into three groups based on phylogenetic analysis and eight subfamilies based on special domains in common walnut. These common walnut F-box genes are distributed on 31 different pseudo-chromosomes. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and microRNA profiles showed that the F-box gene family might play a critical role in the flowering of common walnut. The expressions were significantly higher in female flowers and male flowers compared with leaf and hull tissues at a transcriptome level. The results revealed that the expressions of the F-box gene in female flowers were positively correlated with male flowers, but there was no correlation between any other tissue combinations in common walnut. Our results provided insight into the general characteristics of the F-box genes in common walnut.

scholarly journals Transcriptome-Wide Identification and Characterization of the JAZ Gene Family in Mentha canadensis L.

2021 ◽  
Vol 22 (16) ◽  
pp. 8859 ◽  
Author(s):  
Dong-Bei Xu ◽  
Ya-Nan Ma ◽  
Teng-Fei Qin ◽  
Wei-Lin Tang ◽  
Xi-Wu Qi ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Chinese Herb ◽  
Gene Families ◽  
Pcr Analysis ◽  
Potential Candidate ◽  
Dependent Manner ◽  
Meja Treatment ◽  
Localization Analysis ◽  
Ja Signaling

Jasmonate ZIM-domain (JAZ) proteins are the crucial transcriptional repressors in the jasmonic acid (JA) signaling process, and they play pervasive roles in plant development, defense, and plant specialized metabolism. Although numerous JAZ gene families have been discovered across several plants, our knowledge about the JAZ gene family remains limited in the economically and medicinally important Chinese herb Mentha canadensis L. Here, seven non-redundant JAZ genes named McJAZ1–McJAZ7 were identified from our reported M. canadensis transcriptome data. Structural, amino acid composition, and phylogenetic analysis showed that seven McJAZ proteins contained the typical zinc-finger inflorescence meristem (ZIM) domain and JA-associated (Jas) domain as conserved as those in other plants, and they were clustered into four groups (A-D) and distributed into five subgroups (A1, A2, B1, B2, and D). Quantitative real-time PCR (qRT-PCR) analysis showed that seven McJAZ genes displayed differential expression patterns in M. canadensis tissues, and preferentially expressed in flowers. Furthermore, the McJAZ genes expression was differentially induced after Methyl jasmonate (MeJA) treatment, and their transcripts were variable and up- or down-regulated under abscisic acid (ABA), drought, and salt treatments. Subcellular localization analysis revealed that McJAZ proteins are localized in the nucleus or cytoplasm. Yeast two-hybrid (Y2H) assays demonstrated that McJAZ1-5 interacted with McCOI1a, a homolog of Arabidopsis JA receptor AtCOI1, in a coronatine-dependent manner, and most of McJAZ proteins could also form homo- or heterodimers. This present study provides valuable basis for functional analysis and exploitation of the potential candidate McJAZ genes for developing efficient strategies for genetic improvement of M. canadensis.

scholarly journals Identification and expression analysis of Tubulin gene family in upland cotton

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Baojun CHEN ◽  
Junjie ZHAO ◽  
Guoyong FU ◽  
Xinxin PEI ◽  
Zhaoe PAN ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Critical Role ◽  
Fiber Development ◽  
Pcr Analysis ◽  
Evolutionary Analysis ◽  
Tubulin Gene ◽  
Core Element ◽  
Protein Motifs ◽  
Seed Epidermis

Abstract Background Cotton fibers are single-celled extensions of the seed epidermis, a model tissue for studying cytoskeleton. Tubulin genes play a critical role in synthesizing the microtubules (MT) as a core element of the cytoskeleton. However, there is a lack of studies concerning the systematic characterization of the tubulin gene family in cotton. Therefore, the identification and portrayal of G. hirsutum tubulin genes can provide key targets for molecular manipulation in cotton breeding. Result In this study, we investigated all tubulin genes from different plant species and identified 98 tubulin genes in G. hirsutum. Phylogenetic analysis showed that tubulin family genes were classified into three subfamilies. The protein motifs and gene structure of α-, β-tubulin genes are more conserved compared with γ-tubulin genes. Most tubulin genes are located at the proximate ends of the chromosomes. Spatiotemporal expression pattern by transcriptome and qRT-PCR analysis revealed that 12 α-tubulin and 7 β-tubulin genes are specifically expressed during different fiber development stages. However, Gh.A03G027200, Gh.D03G169300, and Gh.A11G258900 had differential expression patterns at distinct stages of fiber development in varieties J02508 and ZRI015. Conclusion In this study, the evolutionary analysis showed that the tubulin genes were divided into three clades. The genetic structures and molecular functions were highly conserved in different plants. Three candidate genes, Gh.A03G027200, Gh.D03G169300, and Gh.A11G258900 may play a key role during fiber development complementing fiber length and strength.

scholarly journals Genome-Wide Identification and Transcriptional Expression of the PAL Gene Family in Common Walnut (Juglans Regia L.)

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 46 ◽  
Author(s):  
Feng Yan ◽  
Huaizhu Li ◽  
Peng Zhao
Keyword(s):  
Gene Family ◽  
Juglans Regia ◽  
Expression Patterns ◽  
Critical Role ◽  
Phenylpropanoid Pathway ◽  
Transcriptional Expression ◽  
Genome Wide ◽  
A Genome ◽  
The Common ◽  
Common Walnut

Juglans regia L. is an economically important crop cultivated worldwide for its high quality and quantity of wood and nuts. Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway that plays a critical role in plant growth, development, and adaptation, but there have been few reports of the PAL gene family in common walnut. Here, we report a genome-wide study of J. regia PAL genes and analyze their phylogeny, duplication, microRNA, and transcriptional expression. A total of 12 PAL genes were identified in the common walnut and clustered into two subfamilies based on phylogenetic analysis. These common walnut PALs are distributed on eight different pseudo-chromosomes. Seven of the 12 PALs (JrPAL2-3, JrPAL4-2, JrPAL2-1, JrPAL4-1, JrPAL8, JrPAL9, and JrPAL6) were specific found in J. regia, and JrPAL3, JrPAL5, JrPAL1-2, JrPAL7, and JrPAL2-2 were found to be closely associated with the woody plant Populus trichocarpa. Additionally, the expression patterns of JrPAL3, JrPAL7, JrPAL9, and JrPAL2-1 showed that they had high expression in female and male flowers. The miRNA ath-miR830-5p regulates two genes, JrPAL5 and JrPAL1, such that they have low expression in the male and female flowers of the common walnut. Our research provides useful information for further research into the function of PAL genes in common walnut and Juglans.

scholarly journals Gene Expression Divergence and Evolutionary Analysis of the Drosomycin Gene Family inDrosophila melanogaster

2009 ◽  
Vol 2009 ◽  
pp. 1-9 ◽  
Author(s):  
Xiao-Juan Deng ◽  
Wan-Ying Yang ◽  
Ya-Dong Huang ◽  
Yang Cao ◽  
Shuo-Yang Wen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Binding Sites ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Species Group ◽  
Evolutionary Analysis ◽  
Promoter Regions ◽  
Transcription Start Sites

Drosomycin(Drs) encoding an inducible 44-residue antifungal peptide is clustered with six additional genes,Dro1, Dro2, Dro3, Dro4, Dro5,andDro6, forming a multigene family on the 3L chromosome arm inDrosophila melanogaster. To get further insight into the regulation of each member of the drosomycin gene family, here we investigated gene expression patterns of this family by either microbe-free injury or microbial challenges using real time RT-PCR. The results indicated that among the sevendrosomycingenes,Drs, Dro2, Dro3, Dro4,andDro5showed constitutive expressions. Three out of five,Dro2, Dro3,andDro5, were able to be upregulated by simple injury. Interestingly,Drsis an only gene strongly upregulated whenDrosophilawas infected with microbes. In contrast to these five genes,Dro1andDro6were not transcribed at all in either noninfected or infected flies. Furthermore, by5′rapid amplification of cDNA ends, two transcription start sites were identified inDrsandDro2, and one inDro3, Dro4,andDro5. In addition, NF-κB binding sites were found in promoter regions ofDrs, Dro2, Dro3,andDro5, indicating the importance of NF-κB binding sites for the inducibility ofdrosomycingenes. Based on the analyses of flanking sequences of each gene inD. melanogasterand phylogenetic relationship ofdrosomycinsinD. melanogasterspecies-group, we concluded that gene duplications were involved in the formation of the drosomycin gene family. The possible evolutionary fates ofdrosomycingenes were discussed according to the combining analysis of gene expression pattern, gene structure, and functional divergence of these genes.

scholarly journals Genome-Wide Identification and Characterization of the Trehalose-6-phosphate Synthetase (TPS) Gene Family in Watermelon (Citrullus lanatus) and Their Transcriptional Responses to Salt Stress

2021 ◽  
Vol 23 (1) ◽  
pp. 276
Author(s):  
Gaopeng Yuan ◽  
Junpu Liu ◽  
Guolin An ◽  
Weihua Li ◽  
Wenjing Si ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Gene Family ◽  
Citrullus Lanatus ◽  
Expression Patterns ◽  
Critical Role ◽  
Evolutionary Analysis ◽  
Functional Protein ◽  
Transcriptional Responses

With the increase in watermelon cultivation area, there is an urgent need to explore enzymatic and genetic resources for the sustainable development of watermelon, especially under salt stress. Among the various compounds known, trehalose plays an important role in regulating abiotic stress tolerances in diverse organisms, including plants. Therefore, the present study comprehensively analyzed the trehalose-6-phosphate synthase (TPS) gene family in watermelon. The study analyzed the functional classification, evolutionary characteristics, and expression patterns of the watermelon TPS genes family. Seven ClTPSs were identified and classified into two distinct classes according to gene structure and phylogeny. Evolutionary analysis suggested the role of purifying selection in the evolution of the TPS family members. Further, cis-acting elements related to plant hormones and abiotic stress were identified in the promoter region of the TPS genes. The tissue-specific expression analysis showed that ClTPS genes were widely expressed in roots, stems, leaves, flowers, and fruits, while ClTPS3 was significantly induced under salt stress. The overexpression of ClTPS3 in Arabidopsis thaliana significantly improved salt tolerance. Finally, the STRING functional protein association networks suggested that the transcription factor ClMYB and ClbHLH regulate ClTPS3. Thus, the study indicates the critical role of ClTPS3 in watermelon response to salt stress.

scholarly journals Duplication of the Phytoene Synthase Gene in the Carotenoid Biosynthetic Pathway of Watermelon

HortScience ◽  
2006 ◽  
Vol 41 (4) ◽  
pp. 1007A-1007 ◽  
Author(s):  
Haejeen Bang ◽  
Sunggil Kim ◽  
Daniel I. Leskovar ◽  
Angela Davis ◽  
Stephen R. King
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Gene Expression Pattern ◽  
Gene Families ◽  
Phytoene Synthase ◽  
Pcr Analysis ◽  
Long Time ◽  
Phytoene Synthase Gene ◽  
Relationship Of ◽  
Identification And Characterization

Gene identification and characterization can be utilized for the identification of respective functions and their relationship to flesh color inheritance. Phytoene synthase (PSY), which converts two molecules of GGPP into phytoene, is the first committed step of the pathway. Previous phylogenetic analysis of PSY has indicated that PSY duplication is common in Poaceae, but rare in dicots. Degenerate PCR and RACE were used for PSY cloning. Three members of PSY gene family (PSY-A, PSY-B and PSY-C) were identified. PSY-A shared higher identity with PSY-C than PSY-B. PSYC shared 96% identity with melon PSY. PSY-C also showed a high homology with tomato PSY1, even higher than PSY-A and PSY-B. It showed a similar gene expression pattern, so we propose that PSY-C is a homologue to PSY1. RT-PCR analysis indicated that PSY-B has a different transcriptional behavior from PSY-A, similar to tomato PSY2. Therefore, PSY genes appear to be under different regulatory mechanisms. Deduced protein sequence of PSY1 or PSY2 between species has higher homology than between PSY1 and PSY2 within species. Phylogenetic analysis indicated that watermelon PSY gene family is very distantly related. Watermelon and carrot PSY gene families did not appear to cluster as closely as in Poaceae or tomato. This indicates that watermelon and carrot PSY genes are not conserved as much as PSY in tomato or Poaceae. There was no particular pattern in phylogenetic relationship of dicots. Poaceae PSY genes showed a clustering into a PSY1 group and PSY2 group. PSY duplication in watermelon provides additional evidence that PSY duplication may be a common phenomenon in dicots. They are likely to be duplicated evolutionarily a long time ago, possibly even prior to the evolution of monocot and dicot divergence.

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