Identification and expression analysis of E2 ubiquitin-conjugating enzymes in cucumber

2021 ◽  
Author(s):  
Wei Lai ◽  
Zhaoyang Hu ◽  
Chuxia Zhu ◽  
Yingui Yang ◽  
Shiqiang Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Biological Processes ◽  
Protein Ubiquitination ◽  
Genome Wide ◽  
Conjugating Enzymes ◽  
Gene Structures ◽  
Ubiquitin Conjugating Enzymes ◽  
Genome Wide Survey

Protein ubiquitination is one of the most common modifications that can degrade or modify proteins in eukaryotic cells. The E2 ubiquitin-conjugating enzymes (UBCs) are involved in multiple biological processes of eukaryotes and their response to adverse stresses. Genome-wide survey of the UBC gene family has been performed in many plant species but not in cucumber (Cucumis sativus). In this study, a total of 38 UBC family genes (designated as CsUBC1–CsUBC38) were identified in cucumber. The phylogenetic analysis of UBC proteins from cucumber, Arabidopsis and maize indicated that these proteins could be divided into 15 groups. Most of the phylogenetically related CsUBC members had similar conserved motif patterns and gene structures. The CsUBC genes were unevenly distributed on seven chromosomes, and gene duplication analysis indicated that segmental duplication has played a significant role in the expansion of the cucumber UBC gene family. Promoter analysis of these genes resulted in the identification of many hormone-, stress- and development-related cis-elements. The CsUBC genes exhibited differential expression patterns in different tissues and developmental stages of fruit ripening. In addition, a total of 14 CsUBC genes were differentially expressed upon downy mildew (DM) infection compared with the control. Our results lay the foundation for further clarification of the roles of the CsUBC genes in the future.

scholarly journals Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

2019 ◽  
Author(s):  
Yong Zhou ◽  
Yuan Cheng ◽  
Chunpeng Wan ◽  
Youxin Yang ◽  
Jinyin Chen
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Expression Patterns ◽  
Future Research ◽  
Biological Processes ◽  
Biological Functions ◽  
Specific Expression ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and response to stresses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon-intron structure. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of the nine selected ClDof genes under salt stress and ABA treatments using qRT-PCR, and they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

scholarly journals Genome-Wide Identification and Analysis on YUCCA Gene Family in Isatis indigotica Fort. and IiYUCCA6-1 Functional Exploration

2020 ◽  
Vol 21 (6) ◽  
pp. 2188
Author(s):  
Miaomiao Qin ◽  
Jing Wang ◽  
Tianyi Zhang ◽  
Xiangyang Hu ◽  
Rui Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Control Group ◽  
Binding Motif ◽  
Isatis Indigotica ◽  
Rate Limiting Step ◽  
Genome Wide ◽  
Transgenic Lines ◽  
Gene Structures ◽  
High Auxin

Auxin is one of the most critical hormones in plants. YUCCA (Tryptophan aminotransferase of Arabidopsis (TAA)/YUCCA) enzymes catalyze the key rate-limiting step of the tryptophan-dependent auxin biosynthesis pathway, from IPA (Indole-3-pyruvateacid) to IAA (Indole-3-acetic acid). Here, 13 YUCCA family genes were identified from Isatis indigotica, which were divided into four categories, distributing randomly on chromosomes (2n = 14). The typical and conservative motifs, including the flavin adenine dinucleotide (FAD)-binding motif and flavin-containing monooxygenases (FMO)-identifying sequence, existed in the gene structures. IiYUCCA genes were expressed differently in different organs (roots, stems, leaves, buds, flowers, and siliques) and developmental periods (7, 21, 60, and 150 days after germination). Taking IiYUCCA6-1 as an example, the YUCCA genes functions were discussed. The results showed that IiYUCCA6-1 was sensitive to PEG (polyethylene glycol), cold, wounding, and NaCl treatments. The over-expressed tobacco plants exhibited high auxin performances, and some early auxin response genes (NbIAA8, NbIAA16, NbGH3.1, and NbGH3.6) were upregulated with increased IAA content. In the dark, the contents of total chlorophyll and hydrogen peroxide in the transgenic lines were significantly lower than in the control group, with NbSAG12 downregulated and some delayed leaf senescence characteristics, which delayed the senescence process to a certain extent. The findings provide comprehensive insight into the phylogenetic relationships, chromosomal distributions, and expression patterns and functions of the YUCCA gene family in I. indigotica.

scholarly journals Genome-Wide Analysis of the β-Amylase Gene Family in Brassica L. Crops and Expression Profiles of BnaBAM Genes in Response to Abiotic Stresses

Agronomy ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1855
Author(s):  
Dan Luo ◽  
Ziqi Jia ◽  
Yong Cheng ◽  
Xiling Zou ◽  
Yan Lv
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Sequence Similarity ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Chromosomal Distribution ◽  
Brassica Napus L ◽  
Oil Crops ◽  
Genome Wide ◽  
Gene Structures

The β-amylase (BAM) gene family, known for their property of catalytic ability to hydrolyze starch to maltose units, has been recognized to play critical roles in metabolism and gene regulation. To date, BAM genes have not been characterized in oil crops. In this study, the genome-wide survey revealed the identification of 30 BnaBAM genes in Brassica napus L. (B. napus L.), 11 BraBAM genes in Brassica rapa L. (B. rapa L.), and 20 BoBAM genes in Brassica oleracea L. (B. oleracea L.), which were divided into four subfamilies according to the sequence similarity and phylogenetic relationships. All the BAM genes identified in the allotetraploid genome of B. napus, as well as two parental-related species (B. rapa and B. oleracea), were analyzed for the gene structures, chromosomal distribution and collinearity. The sequence alignment of the core glucosyl-hydrolase domains was further applied, demonstrating six candidate β-amylase (BnaBAM1, BnaBAM3.1-3.4 and BnaBAM5) and 25 β-amylase-like proteins. The current results also showed that 30 BnaBAMs, 11 BraBAMs and 17 BoBAMs exhibited uneven distribution on chromosomes of Brassica L. crops. The similar structural compositions of BAM genes in the same subfamily suggested that they were relatively conserved. Abiotic stresses pose one of the significant constraints to plant growth and productivity worldwide. Thus, the responsiveness of BnaBAM genes under abiotic stresses was analyzed in B. napus. The expression patterns revealed a stress-responsive behaviour of all members, of which BnaBAM3s were more prominent. These differential expression patterns suggested an intricate regulation of BnaBAMs elicited by environmental stimuli. Altogether, the present study provides first insights into the BAM gene family of Brassica crops, which lays the foundation for investigating the roles of stress-responsive BnaBAM candidates in B. napus.

scholarly journals Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Mengyuan Wei ◽  
Aili Liu ◽  
Yujuan Zhang ◽  
Yong Zhou ◽  
Donghua Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Genome Wide ◽  
Gene Structures ◽  
Relationship Of ◽  
Zip Genes

Abstract Background The homeodomain-leucine zipper (HD-Zip) gene family is one of the plant-specific transcription factor families, involved in plant development, growth, and in the response to diverse stresses. However, comprehensive analysis of the HD-Zip genes, especially those involved in response to drought and salinity stresses is lacking in sesame (Sesamum indicum L.), an important oil crop in tropical and subtropical areas. Results In this study, 45 HD-Zip genes were identified in sesame, and denominated as SiHDZ01-SiHDZ45. Members of SiHDZ family were classified into four groups (HD-Zip I-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, which was further supported by the analysis of their conserved motifs and gene structures. Expression analyses of SiHDZ genes based on transcriptome data showed that the expression patterns of these genes were varied in different tissues. Additionally, we showed that at least 75% of the SiHDZ genes were differentially expressed in responses to drought and salinity treatments, and highlighted the important role of HD-Zip I and II genes in stress responses in sesame. Conclusions This study provides important information for functional characterization of stress-responsive HD-Zip genes and may contribute to the better understanding of the molecular basis of stress tolerance in sesame.

scholarly journals Genome-Wide Identification of the Early Flowering 4 (ELF4) Gene Family in Cotton and Silent GhELF4-1 and GhEFL3-6 Decreased Cotton Stress Resistance

2021 ◽  
Vol 12 ◽  
Author(s):  
Miaomiao Tian ◽  
Aimin Wu ◽  
Meng Zhang ◽  
Jingjing Zhang ◽  
Hengling Wei ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Multiple Roles ◽  
Early Flowering ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Gossypium Raimondii ◽  
Spatio Temporal ◽  
Gene Structures

The early flowering 4 (ELF4) family members play multiple roles in the physiological development of plants. ELF4s participated in the plant biological clock’s regulation process, photoperiod, hypocotyl elongation, and flowering time. However, the function in the ELF4s gene is barely known. In this study, 11, 12, 21, and 22 ELF4 genes were identified from the genomes of Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense, respectively. There ELF4s genes were classified into four subfamilies, and members from the same subfamily show relatively conservative gene structures. The results of gene chromosome location and gene duplication revealed that segmental duplication promotes gene expansion, and the Ka/Ks indicated that the ELF4 gene family has undergone purification selection during long-term evolution. Spatio-temporal expression patterns and qRT-PCR showed that GhELF4 genes were mainly related to flower, leaf, and fiber development. Cis-acting elements analysis and qRT-PCR showed that GhELF4 genes might be involved in the regulation of abscisic acid (ABA) or light pathways. Silencing of GhELF4-1 and GhEFL3-6 significantly affected the height of cotton seedlings and reduced the resistance of cotton. The identification and functional analysis of ELF4 genes in upland cotton provide more candidate genes for genetic modification.

scholarly journals BrCNGC gene family in field mustard: genome-wide identification, characterization, comparative synteny, evolution and expression profiling

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Akram Ali Baloch ◽  
Agha Muhammad Raza ◽  
Shahjahan Shabbir Ahmed Rana ◽  
Saad Ullah ◽  
Samiullah Khan ◽  
...  
Keyword(s):  
Gene Family ◽  
Pseudomonas Syringae ◽  
Plasmodiophora Brassicae ◽  
Expression Patterns ◽  
Chemical Properties ◽  
Evolutionary Model ◽  
Phylogenetic Groups ◽  
Genome Wide ◽  
Physico Chemical ◽  
Gene Structures

AbstractCNGCs are ligand-gated calcium signaling channels, which participate in important biological processes in eukaryotes. However, the CNGC gene family is not well-investigated in Brassica rapa L. (i.e., field mustard) that is economically important and evolutionary model crop. In this study, we systematically identified 29 member genes in BrCNGC gene family, and studied their physico-chemical properties. The BrCNGC family was classified into four major and two sub phylogenetic groups. These genes were randomly localized on nine chromosomes, and dispersed into three sub-genomes of B. rapa L. Both whole-genome triplication and gene duplication (i.e., segmental/tandem) events participated in the expansion of the BrCNGC family. Using in-silico bioinformatics approaches, we determined the gene structures, conserved motif compositions, protein interaction networks, and revealed that most BrCNGCs can be regulated by phosphorylation and microRNAs of diverse functionality. The differential expression patterns of BrCNGC genes in different plant tissues, and in response to different biotic, abiotic and hormonal stress types, suggest their strong role in plant growth, development and stress tolerance. Notably, BrCNGC-9, 27, 18 and 11 exhibited highest responses in terms of fold-changes against club-root pathogen Plasmodiophora brassicae, Pseudomonas syringae pv. maculicola, methyl-jasmonate, and trace elements. These results provide foundation for the selection of candidate BrCNGC genes for future breeding of field mustard.

Identification of stress repressive zinc finger gene family and its expression analysis in rice under abiotic constraints

2020 ◽  
Author(s):  
Chao Zhang ◽  
Yanning Tan ◽  
Jemaa Essemine ◽  
Ni Li ◽  
Zhongxiao Hu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Zinc Finger ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Rt Pcr ◽  
Conserved Domains ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Survey

Abstract Background: Stress repressive zinc finger (SRZ) gene family in rice is one of the plant defense gene families that play a pivotal role in plant growth regulation and development, particularly under stressful conditions. However, there is no genome-wide survey regarding SRZ gene family in rice (OsSRZ) till date. Results: We studied, herein, this gene family by performing a genome-wide screening and we identified 25 OsSRZ gene members using Japonica cultivar as an investigating material. Their chromosome localizations, phylogenetic relationships, genomic structures, conserved domains and promoter cis-regulatory elements were analyzed. Besides, their spatio-temporal expression profiles and expression patterns under various hormones and stress treatments were also assessed. Based on the phylogeny and domain constitution, the OsSRZ gene family was classified into five groups (I-V). Conserved domains analysis demonstrates that OsSRZ proteins contain at least one highly conserved SRZ domain. The analysis of expression patterns of the SRZ gene family reveal that OsSRZ genes display tissue-specific expression patterns at various rice developmental stages and exhibit differential responses to both phytohormones and abiotic stresses. Furthermore, q-RT-PCR analysis reveals that Os SRZ genes exhibit different expression patterns under various abiotic stresses. We notice the presence of a single specific gene considerably or strongly up-regulated for each kind of abiotic stress. Over 12 OsSRZ genes analyzed with q-RT-PCR, solely 4 genes (OsSRZ 1, 2, 10 and 11) were found to be substantially or strongly up-regulated following abiotic stress. Notably, OsSRZ 10 and 11 were up-regulated under heat stress by 7 and 5 times, respectively. However, OsSRZ2 was up-regulated by 7 and 3.5 folds under salt and cold stresses, respectively. Interestingly, OsSRZ1 was up-regulated by about 3~11 times in 24 h following artificial oxidative stress application using 1 mM H2O2 . Conclusions: We deduce that some members of OsSRZ gene family function as abiotic stress marker in rice. At the genomic level and expression pattern, our genome-wide survey could provide promising and valuable insights to widen and strengthen further future investigation by leading a cutting edge research regarding the biological and molecular functions of this gene family.

scholarly journals Comprehensive Genomic Characterization and Expression Analysis of the Lipoxygenase Gene Family in Watermelon under Hormonal Treatments

Agriculture ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 429
Author(s):  
Jianping Liu ◽  
Yong Zhou ◽  
Jingwen Li ◽  
Feng Wang ◽  
Youxin Yang
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Protein Structures ◽  
Promoter Regions ◽  
Element Analysis ◽  
Cis Element ◽  
Genome Wide ◽  
Genomic Characterization ◽  
Gene Structures ◽  
Lipoxygenase Gene Family

Lipoxygenases (LOXs) are non-haem iron-containing dioxygenases and play vital roles in a variety of plant biological processes. Here, we first carried out the genome-wide identification of LOX genes in watermelon. A total of 16 LOX genes were identified, which could be classified into two categories according to phylogenetic analysis: the 9-LOXs (ClLOX1–4, 12, and 15) and 13-LOXs (ClLOX5–11, 13, 14, and 16). Furthermore, the protein structures, intrachromosomal distributions, and gene structures were thoroughly analyzed. Cis-element analysis of the promoter regions indicated that the expression of ClLOX genes may be influenced by stress and plant hormones. Bioinformatic and expression analyses revealed that the expression of ClLOX genes is tissue-specific and hormone-responsive. The detected LOX genes exhibited distinctive expression patterns in various tissues. Different ClLOX genes showed different responses to methyl jasmonate (MeJA), salicylic acid (SA), and ethylene (ET) treatments, particularly ClLOX7, which exhibited the most active response to the above treatments. This study provides valuable information for a better understanding of the functions of LOX genes and further exploration of the LOX gene family in watermelon.

scholarly journals Genome-wide systematic characterization of the HAK/KUP/KT gene family and its expression profile during plant growth and in response to low-K+ stress in Saccharum

2019 ◽  
Author(s):  
Xiaomin Feng ◽  
Yongjun Wang ◽  
Nannan Zhang ◽  
Zilin Wu ◽  
Qiaoying Zeng ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Divergence Time ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Duplication Events ◽  
Gene Structures ◽  
Gain Loss ◽  
Low K

Abstract Background: Plant genomes contain a large number of HAK/KUP/KT transporters, which play important roles in potassium uptake and translocation, osmotic potential regulation, salt tolerance, root morphogenesis and plant development. Potassium deficiency in the soil of a sugarcane planting area is serious. However, the HAK/KUP/KT gene family remains to be characterized in sugarcane (Saccharum). Results: In this study, 30 HAK/KUP/KT genes were identified in Saccharum spontaneum. Phylogenetics, duplication events, gene structures and expression patterns were analyzed. Phylogenetic analysis of the HAK/KUP/KT genes from 15 representative plants showed that this gene family is divided into four groups (clades I-IV). Both ancient whole-genome duplication (WGD) and recent gene duplication contributed to the expansion of the HAK/KUP/KT gene family. Nonsynonymous to synonymous substitution ratio (Ka/Ks) analysis showed that purifying selection was the main force driving the evolution of HAK/KUP/KT genes. The divergence time of the HAK/KUP/KT gene family was estimated to range from 134.8 to 233.7 Mya based on Ks analysis, suggesting that it is an ancient gene family in plants. Gene structure analysis showed that the HAK/KUP/KT genes were accompanied by intron gain/loss in the process of evolution. RNA-seq data analysis demonstrated that the HAK/KUP/KT genes from clades II and III were mainly constitutively expressed in various tissues, while most genes from clades I and IV had no or very low expression in the tested tissues at different developmental stages. The expression of SsHAK1 and SsHAK21 was upregulated in response to low-K+ stress. Yeast functional complementation analysis revealed that SsHAK1 and SsHAK21 could rescue K+ uptake in a yeast mutant. Conclusions: This study provided insights into the evolutionary history of HAK/KUP/KT genes. HAK7/9/18 were mainly expressed in the upper photosynthetic zone and mature zone of the stem. HAK7/9/18/25 were regulated by sunlight. SsHAK1 and SsHAK21 played important roles in mediating potassium acquisition under limited K+ supply. Our results provide valuable information and key candidate genes for further studies on the function of HAK/KUP/KT genes in Saccharum. Keywords: Saccharum, HAK/KUP/KT, evolution, gene expression, low-K+ stress

scholarly journals Genome-wide investigation of malate dehydrogenase gene family in poplar (Populus trichocarpa) and their expression analysis under salt stress

2019 ◽  
Author(s):  
Xinghao Chen ◽  
Jun Zhang ◽  
Chao Zhang ◽  
Shijie Wang ◽  
Minsheng Yang
Keyword(s):  
Salt Stress ◽  
Gene Family ◽  
Malate Dehydrogenase ◽  
Molecular Mechanisms ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Subcellular Location ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structures

Malate dehydrogenase (MDH) is widely distributed in plants and animals, and plays an important role in many metabolic processes. However, there have been few studies on MDH genes in poplar. In this study, 16 MDH gene sequences were identified from the Populus trichocarpa genome and renamed according to their chromosomal locations. Based on phylogenetic analysis, the PtMDH genes were divided into five groups, and genes that grouped together all shared the same subcellular location and had similar sequence lengths, gene structures, and conserved motifs. Two pairs of tandem duplication events and three segmental duplication events involving five genes were identified from the 15 PtMDH genes located on the chromosomes. Each pair of genes had a Ka/Ks ratios <1, indicating that the MDH gene family of P. trichocarpa was purified during evolution. Based on the transcriptome data of P. trichocarpa under salt stress and qRT-PCR verification, the expression patterns of PtMDH genes under salt stress were analyzed. The results showed that most of the genes were upregulated under salt stress, indicating that they play a role in the response of poplar to salt stress. The PtmMDH1 gene can be used as an important salt-tolerant candidate gene for further investigations of molecular mechanisms. This study lays the foundation for functional analysis of MDH genes and genetic improvement in poplar.

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