scholarly journals Genome-Wide Characterization of GRAS Family and Their Potential Roles in Cold Tolerance of Cucumber (Cucumis sativus L.)

2020 ◽  
Vol 21 (11) ◽  
pp. 3857 ◽  
Author(s):  
Xiaohong Lu ◽  
Wenqian Liu ◽  
Chenggang Xiang ◽  
Xiaojun Li ◽  
Qing Wang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Gene Family ◽  
Cold Tolerance ◽  
Cucumis Sativus ◽  
Expression Patterns ◽  
Cold Treatment ◽  
Evolutionary Tree ◽  
Cucumis Sativus L ◽  
Gras Family ◽  
Biological Stress

Cucumber (Cucumis sativus L.) is one of the most important cucurbit vegetables but is often subjected to stress during cultivation. GRAS (gibberellic acid insensitive, repressor of GAI, and scarecrow) genes encode a family of transcriptional factors that regulate plant growth and development. In the model plant Arabidopsis thaliana, GRAS family genes function in formation of axillary meristem and root radial structure, phytohormone (gibberellin) signal transduction, light signal transduction and abiotic/biological stress. In this study, a gene family was comprehensively analyzed from the aspects of evolutionary tree, gene structure, chromosome location, evolutionary and expression pattern by means of bioinformatics; 37 GRAS gene family members have been screened from cucumber. We reconstructed an evolutionary tree based on multiple sequence alignment of the typical GRAS domain and conserved motif sequences with those of other species (A. thaliana and Solanum lycopersicum). Cucumber GRAS family was divided into 10 groups according to the classification of Arabidopsis and tomato genes. We conclude that tandem and segmental duplication have played important roles in the expansion and evolution of the cucumber GRAS (CsaGRAS) family. Expression patterns of CsaGRAS genes in different tissues and under cold treatment, combined with gene ontology annotation and interaction network analysis, revealed potentially different functions for CsaGRAS genes in response to cold tolerance, with members of the SHR, SCR and DELLA subfamilies likely playing important roles. In conclusion, this study provides valuable information and candidate genes for improving cucumber tolerance to cold stress.

scholarly journals Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 494 ◽  
Author(s):  
Xiaokang Zhuo ◽  
Tangchun Zheng ◽  
Zhiyong Zhang ◽  
Yichi Zhang ◽  
Liangbao Jiang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Gene Family ◽  
Cold Tolerance ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Freezing Stress ◽  
Prunus Mume ◽  
Flower Bud ◽  
Freezing Resistance

NAC transcription factors (TFs) participate in multiple biological processes, including biotic and abiotic stress responses, signal transduction and development. Cold stress can adversely impact plant growth and development, thereby limiting agricultural productivity. Prunus mume, an excellent horticultural crop, is widely cultivated in Asian countries. Its flower can tolerate freezing-stress in the early spring. To investigate the putative NAC genes responsible for cold-stress, we identified and analyzed 113 high-confidence PmNAC genes and characterized them by bioinformatics tools and expression profiles. These PmNACs were clustered into 14 sub-families and distributed on eight chromosomes and scaffolds, with the highest number located on chromosome 3. Duplicated events resulted in a large gene family; 15 and 8 pairs of PmNACs were the result of tandem and segmental duplicates, respectively. Moreover, three membrane-bound proteins (PmNAC59/66/73) and three miRNA-targeted genes (PmNAC40/41/83) were identified. Most PmNAC genes presented tissue-specific and time-specific expression patterns. Sixteen PmNACs (PmNAC11/19/20/23/41/48/58/74/75/76/78/79/85/86/103/111) exhibited down-regulation during flower bud opening and are, therefore, putative candidates for dormancy and cold-tolerance. Seventeen genes (PmNAC11/12/17/21/29/42/30/48/59/66/73/75/85/86/93/99/111) were highly expressed in stem during winter and are putative candidates for freezing resistance. The cold-stress response pattern of 15 putative PmNACs was observed under 4 °C at different treatment times. The expression of 10 genes (PmNAC11/20/23/40/42/48/57/60/66/86) was upregulated, while 5 genes (PmNAC59/61/82/85/107) were significantly inhibited. The putative candidates, thus identified, have the potential for breeding the cold-tolerant horticultural plants. This study increases our understanding of functions of the NAC gene family in cold tolerance, thereby potentially intensifying the molecular breeding programs of woody plants.

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

2019 ◽  
Vol 20 (21) ◽  
pp. 5309 ◽  
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.

scholarly journals Genome-wide identification and characterization of lectin receptor-like kinase gene family in cucumber and expression profiling analysis under different treatments

2020 ◽  
Author(s):  
Duo Lv ◽  
Gang Wang ◽  
Yue Chen ◽  
Liang-Rong Xiong ◽  
Jing-Xian Sun ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Kinase Gene ◽  
Cucumis Sativus L ◽  
Lectin Receptor ◽  
Genome Wide ◽  
Cucumber Genome ◽  
And Function

Abstract Background Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber ( Cucumis sativus L.).Results In this study, 46 putative LecRLK genes were identified in cucumber genome, including 23 G-type, 22 L-type and 1 C-type LecRLK genes. They unequally distributed on all 7 chromosomes with a clustering trendency. Most of the genes in the cucumber LecRLK (Cs LecRLK) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormone and stress on these genes’ promoters. Transcriptome data demonstrated that distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real time PCR (qRT-PCR) analysis.Conclusion This study provides a better understanding of the evolution and function of LecRLK gene family in cucumber, and opens the possibility to explore the roles that LecRLK s might play in the life cycle of cucumber.

scholarly journals Transcriptome analysis of ovary culture-induced embryogenesis in cucumber (Cucumis sativus L.)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12145
Author(s):  
Ying Deng ◽  
Wenyuan Fu ◽  
Bing Tang ◽  
Lian Tao ◽  
Lu Zhang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Plant Regeneration ◽  
Cucumis Sativus ◽  
Transcriptome Sequencing ◽  
Shoot Formation ◽  
Early Embryo ◽  
Ovary Culture ◽  
Cucumis Sativus L ◽  
Microtubule Binding ◽  
Time Points

Background. Ovary culture is a useful technique used to generate double haploid (DH) cucumber (Cucumis sativus L.) plants. However, cucumber ovary culture have a low rate of embryo induction and plant regeneration. Moreover, the cucumber embryogenesis mechanism remains unclear. In this study, we explored the molecular basis of cucumber embryogenesis in order to establish a foundation for a more efficient ovary culture method. Using transcriptome sequencing, we also investigated the differential expression of genes during the embryogenesis process. Methods. Cytological and morphological observations have divided cucumber ovary culture into three stages: early embryo development (T0), embryo morphogenesis (T1, T2, T3 and T4), and shoot formation (T5). We selected six key time points for transcriptome sequencing and analysis: T0 (the ovules were cultured for 0 d), T1 (the ovules were cultured for 2 d), T2 (the embryos were cultured for 10 d), T3 (the embryos were cultured for 20 d), T4 (the embryos were cultured for 30 d), and T5 (the shoots after 60 d culture). Results. We used cytology and morphology to observe the characteristics of the cucumber’s developmental transformation during embryogenesis and plant regeneration. The differentially expressed genes(DEGs) at developmental transition points were analyzed using transcriptome sequencing. In the early embryogenesis stage, the cells expanded, which was the signal for gametophytes to switch to the sporophyte development pathway. RNA-seq revealed that when compared to the fresh unpollinated ovaries, there were 3,468 up-regulated genes in the embryos, including hormone signal transduction genes, hormone response genes, and stress-induced genes. The reported embryogenesis-related genes BBM, HSP90 and AGL were also actively expressed during this stage. In the embryo morphogenesis stage (from cell division to cotyledon-embryo formation), 480 genes that functioned in protein complex binding, microtubule binding, tetrapyrrole binding, tubulin binding and other microtubule activities were continuously up-regulated during the T1, T2, T3 and T4 time points. This indicated that the cytoskeleton structure was continuously being built and maintained by the action of microtubule-binding proteins and enzyme modification. In the shoot formation stage, 1,383 genes were up-regulated that were mainly enriched in phenylpropanoid biosynthesis, plant hormone signal transduction, phenylalanine metabolism, and starch and sucrose metabolism. These up-regualted genes included six transcription factors that contained a B3 domain, nine genes in the AP2/ERF family, and two genes encoding WUS homologous domain proteins. Conclusions. Evaluation of molecular gynogenesis events may contribute to a better understanding of the molecular mechanism of cucumber ovarian culture.

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 Polymorphism in the Chloroplast ATP Synthase Beta-Subunit Is Associated with a Maternally Inherited Enhanced Cold Recovery in Cucumber

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1092
Author(s):  
Madeline W. Oravec ◽  
Michael J. Havey
Keyword(s):  
Cold Tolerance ◽  
Atp Synthase ◽  
Cold Treatment ◽  
Warm Season ◽  
Chloroplast Transformation ◽  
Beta Subunit ◽  
Cucumis Sativus L ◽  
Reciprocal Hybrids ◽  
Cold Tolerant ◽  
Dh Lines

Cucumber (Cucumis sativus L.) is a warm-season crop that is sensitive to chilling temperatures and a maternally inherited cold tolerance exists in the heirloom cultivar ‘Chipper’ (CH). Because the organelles of cucumber show differential transmission (maternal for chloroplast and paternal for mitochondrion), this cold tolerance is hypothesized to be chloroplast-associated. The goal of this research was to characterize the cold tolerant phenotype from CH and determine its genetic basis. Doubled haploid (DH) lines were produced from CH and cold susceptible cucumbers, reciprocal hybrids with identical nuclear genotypes were produced, and plants were subjected to cold treatments under lights at 4 °C for 5.5 h. Hybrid plants with CH as the maternal parent had significantly higher fresh and dry weights 14 days after cold treatment compared to the reciprocal hybrid, revealing an enhanced cold recovery phenotype maternally conferred by CH. Results from analyses of the nuclear transcriptome and reactive oxygen species (ROS) between reciprocal hybrids were consistent with the cold recovery phenotype. Sequencing of the chloroplast genome and transcriptome of the DH parents and reciprocal hybrids, respectively, revealed one maternally transmitted non-synonymous single nucleotide polymorphism (SNP) in the chloroplast F1FO-ATP synthase (CF1FO-ATPase) beta-subunit gene (atpB) of CH which confers an amino acid change from threonine to arginine. Protein modeling revealed that this change is located at the interface of the alpha- and beta-subunits in the CF1FO-ATPase complex. Polymorphisms in the CF1FO-ATPase complex have been associated with stress tolerances in other plants, and selection for or creation of polymorphic beta-subunit proteins by chloroplast transformation or gene editing could condition improved recovery from cold stress in plants.

scholarly journals Analysis of differentially expressed genes during embryogenesis in ovary culture of cucumber (Cucumis sativus L.)

2019 ◽  
Author(s):  
Ying Deng ◽  
Wenyuan Fu ◽  
Bing Tang ◽  
Lian Tao ◽  
Lu Zhang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Cucumis Sativus ◽  
Differentially Expressed Genes ◽  
Shoot Formation ◽  
Differentially Expressed ◽  
Embryo Maturation ◽  
Ovary Culture ◽  
Cucumis Sativus L ◽  
Microtubule Binding ◽  
Formation Stage

Abstract Background: Ovary culture has been a useful way to generate double haploid (DH) plant in cucumber (Cucumis sativus L.). However, the rate of embryo induction is low, and the probability for the induced embryo to grow into normal embryo is low as well. This is largely due to unknown of the mechanism of embryogenesis in cucumber. In this study, the differentially expressed genes during embryogenesis, including the early stages of embryo formation, embryo maturation and shoot formation, was investigated with transcriptomic technique to set up basis for a more efficient ovary culture technology Results: Cytological observations led to suggestions that cell enlargement is the symbol that gametophytes had switched to the sporophyte development pathway during the early embryogenesis stage. In this stage, RNA-seq revealed 3468 up-regulated genes, including hormone signal transduction genes, hormone response genes and stress-induced genes. The reported embryogenesis-related genes BBM, HSP90 and AGL were also actively expressed during this stage. The total of 480 genes that function in protein complex binding, microtubule binding, tetrapyrrole binding, tubulin binding and other microtubule activities were continuously up-regulated during the embryo maturation stage, indicating that the cytoskeleton structure was continuously being built and maintained by the action of microtubule-binding proteins and enzyme modification during embryo development. In the shoot formation stage, 1383 genes were up-regulated, which were mainly enriched in phenylpropanoid biosynthesis, plant hormone signal transduction, phenylalanine metabolism, and starch and sucrose metabolism. The shoot formation stage might be regulated by 6 transcription factors that contained a B3 domain, 9 genes in the AP2/ERF family and 2 genes encoded WUS homologous domain proteins. Conclusions: Findings from this study offer a valuable framework for explaining the transcriptional regulatory mechanism underlying embryogenesis in cucumber ovary culture.

scholarly journals Genome-wide identification and expression analysis of CYP450 gene family in Cucumis sativus L.

2021 ◽  
Author(s):  
hongyu wang ◽  
Pengfei Li ◽  
Yu Wang ◽  
Chunyu Chi ◽  
Guohua Ding
Keyword(s):  
Subcellular Localization ◽  
Gene Family ◽  
Cucumis Sativus ◽  
Expression Profile ◽  
Evolutionary Relationship ◽  
Evolutionary Analysis ◽  
Cucumis Sativus L ◽  
P450 Gene ◽  
Genome Wide ◽  
A Genome

Abstract The cytochrome P450 (CYP450) gene family plays a vital role in basic metabolism and enhances plant resistance to stress and pests. However, little information is available on the genome-wide characterization and evolutionary relationship of the CYP450 gene family in Cucumis sativus L. In the present study, a genome-wide bioinformatics analysis was performed, including gene structure, conserved motif, cis-acting promoter element, evolutionary analysis, collinearity, subcellular localization, and expression profile. The gene expression profile of CYP450 was verified using transcriptome sequencing and quantitative reverse transcription polymerase chain reaction. A total of 165 P450 genes were identified in the cucumber genome. These genes were classified into eight subfamilies and unevenly distributed on seven chromosomes. Subcellular localization predicted that most of P450 genes were located in chloroplasts and a few were located on the plasma membrane. CYP450 genes were differentially expressed in different tissues and in response to salicylic acid (SA) treatment. The sizes of all cucumber P450 proteins ranged from 317 to 1,056 aa, the theoretical isoelectric points ranged from 5.05 to 10.31, and the molecular weights ranged from 36,095 to 121,403 KD. This study provides a theoretical basis for further research on the biological functions of the P450 gene in cucumber plants.

Sign in / Sign up

Export Citation Format

Share Document