scholarly journals Insight into the B3Transcription Factor Superfamily and Expression Profiling of B3 Genes in Axillary Buds after Topping in Tobacco(Nicotiana tabacum L.)

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 164 ◽  
Author(s):  
Fei Xia ◽  
Tingting Sun ◽  
Shuangjuan Yang ◽  
Xiao Wang ◽  
Jiangtao Chao ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Expression Patterns ◽  
Protein Structures ◽  
Axillary Buds ◽  
Comparative Genome Analysis ◽  
Specific Expression ◽  
Protein Motifs ◽  
Nicotiana Tabacum L ◽  
Gene Structures ◽  
Insight Into

Members of the plant-specific B3 transcription factor superfamily play important roles in various growth and developmental processes in plants. Even though there are many valuable studies on B3 genes in other species, little is known about the B3 superfamily in tobacco. We identified 114 B3 proteins from tobacco using comparative genome analysis. These proteins were classified into four subfamilies based on their phylogenetic relationships, and include the ARF, RAV, LAV, and REM subfamilies. The chromosomal locations, gene structures, conserved protein motifs, and sub-cellular localizations of the tobacco B3 proteins were analyzed. The patterns of exon-intron numbers and arrangement and the protein structures of the tobacco B3 proteins were in general agreement with their phylogenetic relationships. The expression patterns of 114 B3 genes revealed that many B3 genes show tissue-specific expression. The expression levels of B3 genes in axillary buds after topping showed that the REM genes are mainly up-regulated in response to topping, while the ARF genes are down-regulated after topping.

scholarly journals Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1848
Author(s):  
Meimei Hu ◽  
Mengdi Li ◽  
Jianbo Wang
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Expression Patterns ◽  
Protein Structures ◽  
Evolutionary Process ◽  
Orthologous Gene ◽  
Evolutionary Relationships ◽  
Protein Motifs ◽  
Gene Pairs ◽  
Gene Structures

SUV (the Suppressor of variegation [Su(var)] homologs and related) gene family is a subgroup of the SET gene family. According to the SRA domain and WIYLD domain distributions, it can be divided into two categories, namely SUVH (the Suppressor of variegation [Su(var)] homologs) and SUVR (the Suppressor of variegation [Su(var)] related). In this study, 139 SUV genes were identified in allopolyploid Brassica napus and its diploid ancestors, and their evolutionary relationships, protein properties, gene structures, motif distributions, transposable elements, cis-acting elements and gene expression patterns were analyzed. Our results showed that the SUV gene family of B. napus was amplified during allopolyploidization, in which the segmental duplication and TRD played critical roles. After the separation of Brassica and Arabidopsis lineages, orthologous gene analysis showed that many SUV genes were lost during the evolutionary process in B. rapa, B. oleracea and B. napus. The analysis of the gene and protein structures and expression patterns of 30 orthologous gene pairs which may have evolutionary relationships showed that most of them were conserved in gene structures and protein motifs, but only four gene pairs had the same expression patterns.

scholarly journals Conservation and Divergence of the CONSTANS-Like (COL) Genes Related to Flowering and Circadian Rhythm in Brassica napus

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuxi Chen ◽  
Rijin Zhou ◽  
Qiong Hu ◽  
Wenliang Wei ◽  
Jia Liu
Keyword(s):  
Brassica Napus ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Structures ◽  
Three Dimensional ◽  
Evolutionary Relationship ◽  
Specific Expression ◽  
Circadian Expression ◽  
Photoperiod Pathway ◽  
Gene Structures

The CONSTANS-LIKE (COL) genes are important signaling component in the photoperiod pathway and flowering regulation pathway. However, people still know little about their role in Brassica napus. To achieve a better understanding of the members of the BnaCOL gene family, reveal their evolutionary relationship and related functions involved in photoperiod regulation, we systematically analyzed the BnaCOL family members in B. napus genome. A total of 33 BnaCOL genes distributed unevenly on 16 chromosomes were identified in B. napus and could be classified into three subfamilies. The same subfamilies have relatively conservative gene structures, three-dimensional protein structures and promoter motifs such as light-responsive cis-elements. The collinearity analysis detected 37 pairs of repetitive genes in B. napus genome. A 67.7% of the BnaCOL genes were lost after B. napus genome polyploidization. In addition, the BnaCOL genes showed different tissue-specific expression patterns. A 81.8% of the BnaCOL genes were mainly expressed in leaves, indicating that they may play a conservative role in leaves. Subsequently, we tested the circadian expression profiles of nine homologous genes that regulate flowering in Arabidopsis. Most BnaCOL genes exhibit several types of circadian rhythms, indicating that these BnaCOL genes are involved in the photoperiod pathway. As such, our research has laid the foundation for understanding the exact role of the BnaCOL family in the growth and development of rapeseed, especially in flowering.

Identification of MdDof genes in apple and analysis of their response to biotic or abiotic stress

2018 ◽  
Vol 45 (5) ◽  
pp. 528 ◽  
Author(s):  
Qing Yang ◽  
Qiuju Chen ◽  
Yuandi Zhu ◽  
Tianzhong Li
Keyword(s):  
Abiotic Stress ◽  
Zinc Finger ◽  
Flower Development ◽  
Higher Plants ◽  
Expression Patterns ◽  
Fruit Trees ◽  
Biological Processes ◽  
Protein Motifs ◽  
Gene Structures ◽  
Dof Transcription Factors

As a classic plant-specific transcription factor family – the Dof domain proteins – are involved in a variety of biological processes in organisms ranging from unicellular Chlamydomonas to higher plants. However, there are limited reports of MdDof (Malus domestica Borkh. DNA-binding One Zinc Finger) domain proteins in fruit trees, especially in apple. In this study we identified 54 putative Dof transcription factors in the apple genome. We analysed the gene structures, protein motifs, and chromosome locations of each of the MdDof genes. Next, we characterised all 54 MdDofs their expression patterns under different abiotic and biotic stress conditions. It was found that MdDof6,26 not only played an important role in the biotic/abiotic stress but may also be involved in many molecular functions. Further, both in flower development and pollen tube growth it was found that the relative expression of MdDof24 increased rapidly, also with gene ontology analysis it was indicated that MdDof24 was involved in the chemical reaction and flower development pathways. Taken together, our results provide useful clues as to the function of MdDof genes in apple and serve as a reference for studies of Dof zinc finger genes in other plants.

scholarly journals Genome-Wide Identification of Aluminum-Activated Malate Transporter (ALMT) Gene Family in Rubber Trees (Hevea brasiliensis) Highlights Their Involvement in Aluminum Detoxification

Forests ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 142
Author(s):  
Xiaowei Ma ◽  
Feng An ◽  
Lifeng Wang ◽  
Dong Guo ◽  
Guishui Xie ◽  
...  
Keyword(s):  
Hevea Brasiliensis ◽  
Phylogenetic Relationships ◽  
Expression Patterns ◽  
Rubber Tree ◽  
Pcr Analysis ◽  
Cis Elements ◽  
Conserved Motifs ◽  
Gene Structures ◽  
Different Tissues ◽  
Malate Transporter

The rubber tree (Hevea brasiliensis) is a widely cultivated crop in tropical acidic soil that is tolerant to high concentration of aluminum and the aluminum-activated malate transporter (ALMT) plays an important role in plant aluminum detoxification. However, the effects of ALMT on rubber tree aluminum tolerance, growth performance, and latex production are unclear. In this study, 17 HbALMT genes were identified from the genome of rubber trees. The physiological and biochemical characteristics, phylogenetic relationships, gene structures, conserved motifs, cis-elements of promoter, and expression patterns of the identified HbALMT genes were studied. Phylogenetic relationships indicated that these genes were divided into four clusters and genes in the same cluster have similar gene structures and conserved motifs. The promoters of HbALMT genes contain many cis-elements associated with biotic stress and abiotic stress. Quantitative real-time PCR analysis revealed HbALMTs showed various expression patterns in different tissues, indicating the functional diversity of HbALMT genes in different tissues of rubber trees. Transcriptome analysis and qRT-PCR assay showed that most of the HbALMT genes responded to aluminum stress, and among the 17 HbALMTs, HbALMT1, HbALMT2, HbALMT13, and HbALMT15 displayed higher expression levels in roots after two or five days of Al treatments, indicating their potential involvement in aluminum detoxification. Taken together, this study laid a foundation for further understanding the molecular evolution of the ALMT genes and their involvement in rubber tree aluminum adaption.

scholarly journals Genome-Wide Identification and Characterization of the OPR Gene Family in Wheat (Triticum aestivum L.)

2019 ◽  
Vol 20 (8) ◽  
pp. 1914 ◽  
Author(s):  
Yifei Mou ◽  
Yuanyuan Liu ◽  
Shujun Tian ◽  
Qiping Guo ◽  
Chengshe Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Defense Responses ◽  
High Yield ◽  
Flavin Mononucleotide ◽  
Duplicated Genes ◽  
Old Yellow Enzyme ◽  
Specific Expression ◽  
Protein Motifs

The 12-oxo-phytodienoic acid reductases (OPRs), which belong to the old yellow enzyme (OYE) family, are flavin mononucleotide (FMN)-dependent oxidoreductases with critical functions in plants. Despite the clear characteristics of growth and development, as well as the defense responses in Arabidopsis, tomato, rice, and maize, the potential roles of OPRs in wheat are not fully understood. Here, forty-eight putative OPR genes were found and classified into five subfamilies, with 6 in sub. I, 4 in sub. II, 33 in sub. III, 3 in sub. IV, and 2 in sub. V. Similar gene structures and conserved protein motifs of TaOPRs in wheat were identified in the same subfamilies. An analysis of cis-acting elements in promoters revealed that the functions of OPRs in wheat were mostly related to growth, development, hormones, biotic, and abiotic stresses. A total of 14 wheat OPR genes were identified as tandem duplicated genes, while 37 OPR genes were segmentally duplicated genes. The expression patterns of TaOPRs were tissue- and stress-specific, and the expression of TaOPRs could be regulated or induced by phytohormones and various stresses. Therefore, there were multiple wheat OPR genes, classified into five subfamilies, with functional diversification and specific expression patterns, and to our knowledge, this was the first study to systematically investigate the wheat OPR gene family. The findings not only provide a scientific foundation for the comprehensive understanding of the wheat OPR gene family, but could also be helpful for screening more candidate genes and breeding new varieties of wheat, with a high yield and stress resistance.

scholarly journals Genome-Wide Identification, Expansion Mechanism and Expression Profiling Analysis of GLABROUS1 Enhancer-Binding Protein (GeBP) Gene Family in Gramineae Crops

2021 ◽  
Vol 22 (16) ◽  
pp. 8758
Author(s):  
Jishuai Huang ◽  
Qiannan Zhang ◽  
Yurong He ◽  
Wei Liu ◽  
Yanghong Xu ◽  
...  
Keyword(s):  
Gene Family ◽  
Profile Analysis ◽  
Binding Protein ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Limited Information ◽  
Protein Motifs ◽  
Biotic Stresses ◽  
Enhancer Binding Protein ◽  
Gene Structures

The GLABROUS1 enhancer-binding protein (GeBP) gene family encodes a typical transcription factor containing a noncanonical Leucine (Leu-)-zipper motif that plays an essential role in regulating plant growth and development, as well as responding to various stresses. However, limited information on the GeBP gene family is available in the case of the Gramineae crops. Here, 125 GeBP genes from nine Gramineae crops species were phylogenetically classified into four clades using bioinformatics analysis. Evolutionary analyses showed that whole genome duplication (WGD) and segmental duplication play important roles in the expansion of the GeBP gene family. The various gene structures and protein motifs revealed that the GeBP genes play diverse functions in plants. In addition, the expression profile analysis of the GeBP genes showed that 13 genes expressed in all tested organs and stages of development in rice, with especially high levels of expression in the leaf, palea, and lemma. Furthermore, the hormone- and metal-induced expression patterns showed that the expression levels of most genes were affected by various biotic stresses, implying that the GeBP genes had an important function in response to various biotic stresses. Furthermore, we confirmed that OsGeBP11 and OsGeBP12 were localized to the nucleus through transient expression in the rice protoplast, indicating that GeBPs function as transcription factors to regulate the expression of downstream genes. This study provides a comprehensive understanding of the origin and evolutionary history of the GeBP genes family in Gramineae, and will be helpful in a further functional characterization of the GeBP genes.

scholarly journals Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7605
Author(s):  
Caili Li ◽  
Dongqiao Li ◽  
Hong Zhou ◽  
Jiang Li ◽  
Shanfa Lu
Keyword(s):  
Phenolic Compounds ◽  
Posttranscriptional Regulation ◽  
Salvia Miltiorrhiza ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Systematic Investigation ◽  
Whole Genome Sequence ◽  
Rna Sequences ◽  
Specific Expression ◽  
Gene Structures

Salvia miltiorrhiza is one of the most commonly used traditional Chinese medicine materials. It contains important bioactive phenolic compounds, such as salvianolic acids, flavonoids and anthocyanins. Elucidation of phenolic compound biosynthesis and its regulatory mechanism is of great significance for S. miltiorrhiza quality improvement. Laccases (LACs) are multicopper-containing enzymes potentially involved in the polymerization of phenolic compounds. So far, little has been known about LAC genes in S. miltiorrhiza. Through systematic investigation of the whole genome sequence and transcriptomes of S. miltiorrhiza, we identified 65 full-length SmLAC genes (SmLAC1–SmLAC65). Phylogenetic analysis showed that 62 of the identified SmLACs clustered with LACs from Arabidopsis and Populus trichocarpa in seven clades (C1–C7), whereas the other three fell into one S. miltiorrhiza-specific clade (C8). All of the deduced SmLAC proteins contain four conserved signature sequences and three typical Cu-oxidase domains, and gene structures of most LACs from S. miltiorrhiza, Arabidopsis and P. trichocarpa were highly conserved, however SmLACs encoding C8 proteins showed distinct intron-exon structures. It suggests the conservation and diversity of plant LACs in gene structures. The majority of SmLACs exhibited tissue-specific expression patterns, indicates manifold functions of SmLACs played in S. miltiorrhiza. Analysis of high-throughput small RNA sequences and degradome data and experimental validation using the 5′ RACE method showed that 23 SmLACs were targets of Smi-miR397. Among them, three were also targeted by Smi-miR408. It suggests the significance of miR397 and miR408 in posttranscriptional regulation of SmLAC genes. Our results provide a foundation for further demonstrating the functions of SmLACs in the production of bioactive phenolic compounds in S. miltiorrhiza.

scholarly journals Genome-wide analysis of fatty acid desaturase genes in rice (Oryza sativa L.)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Zhiguo E ◽  
Chen Chen ◽  
Jinyu Yang ◽  
Hanhua Tong ◽  
Tingting Li ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Unsaturated Fatty Acids ◽  
Oryza Sativa L ◽  
Expression Patterns ◽  
Rice Genome ◽  
Regulatory Elements ◽  
Segmental Duplications ◽  
Specific Expression ◽  
Gene Structures

AbstractFatty acid desaturases can catalyze saturated or unsaturated fatty acids to form a double bond at various locations in the hydrocarbon chain. In the present study, a total of 20 full-length desaturase genes were identified from rice genome. An exhaustive analysis was performed to describe their chromosomal locations, gene structures, phylogeny, cis-regulatory elements, sub-cellular localizations and expression patterns. The rice desaturase genes were distributed on ten of 12 chromosomes and phylogenetically classified into six subfamilies with the Arabidopsis counterparts, FAB2, FAD2, FAD3/7/8, FAD6, DES1 and SLD1. Among of them, 9 members were expanded via chromosomal tandem or segmental duplications. The gene structures and motif constituents were evolutionarily conserved in the same subfamilies. The majority of desaturase genes showed tissue-specific expression patterns and response to abiotic stresses and hormones based on microarray data and qRT-PCR analyses. This study will provide useful clues for functional validation of desaturase genes and contribute to produce nutritionally important fatty acids by genetic modification in rice.

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 Identification and Characterization of SQUAMOSA—Promoter-Binding Protein (SBP) Genes Involved in the Flowering Development of Citrus Clementina

Biomolecules ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 66 ◽  
Author(s):  
Ren-Fang Zeng ◽  
Jing-Jing Zhou ◽  
Sheng-Rui Liu ◽  
Zhi-Meng Gan ◽  
Jin-Zhi Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Floral Induction ◽  
Binding Protein ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Specific Expression ◽  
Water Deficits ◽  
Citrus Clementina ◽  
Squamosa Promoter Binding Protein ◽  
Gene Structures

SQUAMOSA-promoter binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play vital roles in plant growth and development. In this study, 15 SBP-box genes were identified and isolated from Citrus clementina (CclSBPs), where 10 of these genes were predicted to be putative targets of Citrus clementina microRNA156 (CclmiR156). The 15 CclSBP genes could be classified into six groups based on phylogenetic analysis, diverse intron–exon structure, and motif prediction, similar to the SQUAMOSA promoter binding protein-like (SPL) gene family of Populus trichocarpa and Arabidopsis thaliana. Furthermore, CclSBPs classified into a group/subgroup have similar gene structures and conserved motifs, implying their functional redundancy. Tissue-specific expression analysis of CclSBPs demonstrated their diversified expression patterns. To further explore the potential role of CclSBPs during floral inductive water deficits, the dynamic changes of the 15 CclSBPs were investigated during floral inductive water deficits, and the results showed that some CclSBPs were associated with floral induction. Among these genes, CclSBP6 was not homologous to the Arabidopsis SBP-box gene family, and CclSBP7 was regulated by being alternatively spliced. Therefore, CclSBP6 and CclSBP7 were genetically transformed in Arabidopsis. Overexpression of the two genes changed the flowering time of Arabidopsis.

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