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 Genome-Wide Analysis of the Thioredoxin Gene Family in Gossypium hirsutum L. and the Role of the Atypical Thioredoxin Gene GhTRXL3-2 in Flowering

2021 ◽  
Author(s):  
Hui Liu ◽  
Yunfei Li ◽  
Xianzhong Huang
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Family ◽  
Growth And Development ◽  
Structural Characteristics ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Whole Genome Sequence ◽  
Evolutionary Analysis ◽  
Specific Expression ◽  
Flowering Regulation

AbstractThioredoxin (TRX) is a highly conserved low-molecular-weight protein and a ubiquitous antioxidant enzyme that plays key role in the regulation of plant growth and development. Here, using the whole-genome sequence, we performed a systematic analysis for the TRX gene family in upland cotton (Gossypium hirsutum L.) and analyzed their structural characteristics, evolution, and expression profiles during growth and development. At least 86 GhTRX members, 40 typical and 46 atypical, were identified in the cotton genome, and they were unevenly distributed on the 26 chromosomes. Conserved domains and phylogenic tree construction classified the typical TRX gene family into seven subfamilies and the atypical TRX into nine subfamilies. An evolutionary analysis revealed that the TRX gene family underwent purification selection during evolution. In addition, an RNA-Seq analysis showed that, during vegetative and reproductive development, the differences in transcript abundance levels and organ-specific expression patterns suggest functional diversity. Biochemical assays demonstrated that the atypical TRX protein GhTRXL3-2 interacted with the cotton FLOWERING LOCUS T protein GhFT. The overexpression of GhTRXL3-2 in Arabidopsis thaliana resulted in early flowering compared with control plants. Additionally, the silencing of GhTRXL3-2 in cotton delayed maturation, suggesting that it has important roles in cotton’s flowering regulation. These results help clarify the evolution of the TRX genes and elucidate their biological functions in cotton flowering regulation.

scholarly journals Analysis of the ASMT Gene Family in Pepper (Capsicum annuum L.): Identification, Phylogeny, and Expression Profiles

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Luzhao Pan ◽  
Jiaqiu Zheng ◽  
Jia Liu ◽  
Jun Guo ◽  
Fawan Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Capsicum Annuum ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Pepper Plant ◽  
Rna Seq ◽  
Qrt Pcr ◽  
Group I

Acetylserotonin methyltransferase (ASMT) in plant species, one of the most important enzymes in melatonin biosynthesis, plays a rate-limiting role in the melatonin production. In this study, based on the whole genome sequence, we performed a systematic analysis for the ASMT gene family in pepper (Capsicum annuum L.) and analyzed their expression profiles during growth and development, as well as abiotic stresses. The results showed that at least 16 CaASMT genes were identified in the pepper genome. Phylogenetic analyses of all the CaASMTs were divided into three groups (group I, group II, and group III) with a high bootstrap value. Through the online MEME tool, six distinct motifs (motif 1 to motif 6) were identified. Chromosome location found that most CaASMT genes were mapped in the distal ends of the pepper chromosomes. In addition, RNA-seq analysis revealed that, during the vegetative and reproductive development, the difference in abundance and distinct expression patterns of these CaASMT genes suggests different functions. The qRT-PCR analysis showed that high abundance of CaASMT03, CaASMT04, and CaASMT06 occurred in mature green fruit and mature red fruit. Finally, using RNA-seq and qRT-PCR technology, we also found that several CaASMT genes were induced under abiotic stress conditions. The results will not only contribute to elucidate the evolutionary relationship of ASMT genes but also ascertain the biological function in pepper plant response to abiotic stresses.

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 Characterization of Polygalacturonase Gene Family in Maize (Zea mays L.)

2021 ◽  
Vol 22 (19) ◽  
pp. 10722
Author(s):  
Lu Lu ◽  
Quancan Hou ◽  
Linlin Wang ◽  
Tianye Zhang ◽  
Wei Zhao ◽  
...  
Keyword(s):  
Zea Mays ◽  
Gene Family ◽  
Zea Mays L ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Evolutionary Relationship ◽  
Segmental Duplications

Polygalacturonase (PG, EC 3.2.1.15) is a crucial enzyme for pectin degradation and is involved in various developmental processes such as fruit ripening, pollen development, cell expansion, and organ abscission. However, information on the PG gene family in the maize (Zea mays L.) genome and the specific members involved in maize anther development are still lacking. In this study, we identified 55 PG family genes from the maize genome and further characterized their evolutionary relationship and expression patterns. Phylogenetic analysis revealed that ZmPGs are grouped into six Clades, and gene structures of the same Clade are highly conserved, suggesting their functional conservation. The ZmPGs are randomly distributed across maize chromosomes, and collinearity analysis showed that many ZmPGs might be derived from tandem duplications and segmental duplications, and these genes are under purifying selection. Furthermore, gene expression analysis provided insights into possible functional divergence among ZmPGs. Based on the RNA-seq data analysis, we found that many ZmPGs are expressed in various tissues while 18 ZmPGs are highly expressed in maize anther, and their detailed expression profiles in different anther developmental stages were further investigated by using RT-qPCR analysis. These results provide valuable information for further functional characterization and application of the ZmPGs in maize.

Mediterranean fruit fly genes exhibit different expression patterns between heat and cold treatments

2021 ◽  
pp. 1-7
Author(s):  
Kay Anantanawat ◽  
Alexie Papanicolaou ◽  
Kelly Hill ◽  
Wei Xu
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Insect Pest ◽  
Expression Patterns ◽  
Critical Role ◽  
Cold Treatment ◽  
Fruit Fly ◽  
Mediterranean Fruit Fly ◽  
Molecular Response

Abstract Invasive Tephritid fruit flies are a global threat to both agriculture and horticulture industries. Biosecurity has played a critical role in reducing their damage but becomes more and more challenging after several key chemical pesticides were banned or withdrawn for health or environmental reasons. This has led to non-chemical approaches including heat and cold treatments being broadly utilized to get rid of fruit fly infestation. However, the molecular mechanisms to kill the flies underlying these stressors are not clear yet. This knowledge will certainly help refine current post-harvest treatment strategies and develop more efficient, cost-effective and environmentally friendly approaches for fruit fly management. Previously, the molecular response of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann) to heat was examined thoroughly, in which 31 key genes were identified with significant changes in expression levels and their high-resolution expression timeline was constructed across 11 timepoints. However, whether these candidate genes respond to cold in the same way was unknown. Here, a temperature bioassay was conducted and the expression profiles of these genes were investigated across the same 11 timepoints using cold treatment. The results showed that most of candidate genes exhibited divergent expression profiles compared to heat treatment, suggesting that the fly molecular response to cold may be different from those to heat. This study provides new knowledge of Tephritid fruit fly response to cold at a molecular level, which could aid in improving current fruit fly management and facilitate the development of new strategies to control this serious horticultural insect pest.

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 Genome-wide Identification of the Class III POD Gene Family and their Expression Profiling in Grapevine (Vitisvinifera L)

2020 ◽  
Author(s):  
Huilin Xiao ◽  
Chaoping Wang ◽  
Nadeem Khan ◽  
Mengxia Chen ◽  
Weihong Fu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Critical Role ◽  
Chromosomal Mapping ◽  
Integrated Analysis ◽  
Specific Response ◽  
Evolutionary Analysis ◽  
Class Iii ◽  
Gene Pairs ◽  
Genome Wide

Abstract Background : The class III peroxidases (PODs) are involved in a broad range of physiological activities, such as the formation of lignin, cell wall components, defense against pathogenicity or herbivore, and abiotic stress tolerance. The POD family members have been well-studied and characterized by bioinformatics analysis in several plant species, but no previous genome-wide analysis has been carried out of this gene family in grapevine to date. Results : We comprehensively identified 47 PODs in the grapevine genome and are further classified into 7 subgroups based on their phylogenetic analysis. Results of motif composition and gene structure organization analysis revealed that PODs in the same subgroup shared similar conjunction while the protein sequences were highly conserved. Intriguingly, the integrated analysis of chromosomal mapping and gene collinearity analysis proposed that both dispersed and tandem duplication events contributed to the expansion of PODs in grapevine. Also, the gene duplication analysis suggested that most of the genes (20) were dispersed followed by (15) tandem, (9) segmental or whole-genome duplication, and (3) proximal, respectively. The evolutionary analysis of PODs, such as Ka/Ks ratio of the 15 duplicated gene pairs were less than 1.00, indicated that most of the gene pairs exhibiting purifying selection and 7 pairs underwent positive selection with value greater than 1.00. The Gene Ontology Enrichment (GO), Kyoto Encyclopedia of Genes Genomics (KEGG) analysis, and cis-elements prediction also revealed the positive functions of PODs in plant growth and developmental activities, and response to stress stimuli. Further, based on the publically available RNA-sequence data, the expression patterns of PODs in tissue-specific response during several developmental stages revealed diverged expression patterns. Subsequently, 30 genes were selected for RT-PCR validation in response to (NaCl, drought, and ABA), which showed their critical role in grapevine. Conclusions : In conclusion, we predict that these results will lead to novel insights regarding genetic improvement of grapevine.

scholarly journals Genome-Wide Analysis and Characterization of the Aux/IAA Family Genes Related to Floral Scent Formation in Hedychium coronarium

2019 ◽  
Vol 20 (13) ◽  
pp. 3235 ◽  
Author(s):  
Yanguo Ke ◽  
Farhat Abbas ◽  
Yiwei Zhou ◽  
Rangcai Yu ◽  
Yuechong Yue ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Floral Scent ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Cut Flowers ◽  
Flower Opening ◽  
Hedychium Coronarium

Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.

scholarly journals Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Tandem Repeats ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Genome Wide ◽  
Comprehensive Information ◽  
Family Gene

AbstractMultidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

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.

Sign in / Sign up

Export Citation Format

Share Document