scholarly journals Genome-Wide Identification and Expression Analysis of Sucrose Nonfermenting-1-Related Protein Kinase (SnRK) Genes in Triticum aestivum in Response to Abiotic Stress

2021 ◽  
Author(s):  
Shefali Mishra ◽  
Pradeep Sharma ◽  
Rajender Singh ◽  
ratan Tiwari ◽  
Gyanendra Pratap Singh
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Structural Characteristics ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Plant Stress ◽  
Protein Motif ◽  
Genome Wide

The SnRK gene family is a key regulator playing an important role in plant stress response by phosphorylating the target protein to regulate the signalling pathways. The function of SnRK gene family has been reported in many species but is limited to Triticum asetivum. In this study, SnRK gene family in the wheat genome was identified and its structural characteristics were described. One hundred forty-seven SnRK genes distributed across 21 chromosomes were identified in the Triticum aestivum genome and categorised into three subgroups (SnRK1/2/3) based on phylogenetic analyses and domain types. The gene intron-exon structure and protein-motif composition of SnRKs were similar within each subgroup but different amongst the groups. Gene duplication between the wheat, Arabidopsis, rice and barley genomes was also investigated in order to get insight into the evolutionary aspects of the TaSnRK family genes. SnRK genes showed differential expression patterns in leaves, roots, spike, and grains. Redundant stress-related cis-elements were also found in the promoters of 129 SnRK genes and their expression levels varied widely following drought, ABA and light regulated elements. In particular, TaSnRK2.11 had higher and increased expression under the abiotic stresses and can be a candidate gene for the abiotc stress tolerance. The findings will aid in the functional characterization of TaSnRK genes for further research.

scholarly journals Genome-wide identification and characterization of COMT gene family during the development of blueberry fruit

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yushan Liu ◽  
Yizhou Wang ◽  
Jiabo Pei ◽  
Yadong Li ◽  
Haiyue Sun
Keyword(s):  
Gene Family ◽  
Fruit Development ◽  
Lignin Content ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Vaccinium Corymbosum ◽  
Land Plant ◽  
Phylogenetic Structure ◽  
Genome Wide

Abstract Background Caffeic acid O-methyltransferases (COMTs) play an important role in the diversification of natural products, especially in the phenylalanine metabolic pathway of plant. The content of COMT genes in blueberry and relationship between their expression patterns and the lignin content during fruit development have not clearly investigated by now. Results Ninety-two VcCOMTs were identified in Vaccinium corymbosum. According to phylogenetic analyses, the 92 VcCOMTs were divided into 2 groups. The gene structure and conserved motifs within groups were similar which supported the reliability of the phylogenetic structure groupings. Dispersed duplication (DSD) and whole-genome duplication (WGD) were determined to be the major forces in VcCOMTs evolution. The results showed that the results of qRT-PCR and lignin content for 22 VcCOMTs, VcCOMT40 and VcCOMT92 were related to lignin content at different stages of fruit development of blueberry. Conclusion We identified COMT gene family in blueberry, and performed comparative analyses of the phylogenetic relationships in the 15 species of land plant, and gene duplication patterns of COMT genes in 5 of the 15 species. We found 2 VcCOMTs were highly expressed and their relative contents were similar to the variation trend of lignin content during the development of blueberry fruit. These results provide a clue for further study on the roles of VcCOMTs in the development of blueberry fruit and could promisingly be foundations for breeding blueberry clutivals with higher fruit firmness and longer shelf life.

scholarly journals Genome-Wide Identification and Characterization of Fox Genes in the Honeybee, Apis cerana, and Comparative Analysis with Other Bee Fox Genes

2018 ◽  
Vol 2018 ◽  
pp. 1-12
Author(s):  
Hongyi Nie ◽  
Haiyang Geng ◽  
Yan Lin ◽  
Shupeng Xu ◽  
Zhiguo Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Bombus Terrestris ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Apis Cerana ◽  
Tissue Expression ◽  
Genome Wide ◽  
Fox Genes

The forkhead box (Fox) gene family, one of the most important families of transcription factors, participates in various biological processes. However, Fox genes in Hymenoptera are still poorly known. In this study, 14 Fox genes were identified in the genome of Apis cerana. In addition, 16 (Apis mellifera), 13 (Apis dorsata), 16 (Apis florea), 17 (Bombus terrestris), 16 (Bombus impatiens), and 18 (Megachile rotundata) Fox genes were identified in their genomes, respectively. Phylogenetic analyses suggest that FoxA is absent in the genome of A. dorsata genome. Similarly, FoxG is missing in the genomes A. cerana and A. dorsata. Temporal expression profiles obtained by quantitative real-time PCR revealed that Fox genes have distinct expression patterns in A. cerana, especially for three genes ACSNU03719T0 (AcFoxN4), ACSNU05765T0 (AcFoxB), and ACSNU07465T0 (AcFoxL2), which displayed high expression at the egg stage. Tissue expression patterns showed that FoxJ1 is significantly higher in the antennae of A. cerana and A. mellifera compared to other tissues. These results may facilitate a better understanding of the potential physiological functions of the Fox gene family in A. cerana and provide valuable information for a comprehensive functional analysis of the Fox gene family in Hymenopterans.

scholarly journals Genome-wide identification and characterization of the ALOG gene family in Petunia

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Feng Chen ◽  
Qin Zhou ◽  
Lan Wu ◽  
Fei Li ◽  
Baojun Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Reproductive Organs ◽  
Genome Wide ◽  
Domain Of Unknown Function ◽  
Intron Structure ◽  
Identification And Characterization ◽  
Insight Into

Abstract Background The ALOG (Arabidopsis LSH1 and Oryza G1) family of proteins, namely DUF640 (domain of unknown function 640) domain proteins, were found in land plants. Functional characterization of a few ALOG members in model plants such as Arabidopsis and rice suggested they play important regulatory roles in plant development. The information about its evolution, however, is largely limited, and there was no any report on the ALOG genes in Petunia, an important ornamental species. Results The ALOG genes were identified in four species of Petunia including P. axillaris, P. inflata, P. integrifolia, and P. exserta based on the genome and/or transcriptome databases, which were further confirmed by cloning from P. hybrida ‘W115’ (Mitchel diploid), a popular laboratorial petunia line susceptible to genetic transformation. Phylogenetic analysis indicated that Petunia ALOG genes (named as LSHs according to their closest Arabidopsis homologs) were grouped into four clades, which can be further divided into eight groups, and similar exon-intron structure and motifs are reflected in the same group. The PhLSH genes of hybrid petunia ‘W115’ were mainly derived from P. axillaris. The qPCR analysis revealed distinct spatial expression patterns among them suggesting potentially functional diversification. Moreover, over-expressing PhLSH7a and PhLSH7b in Arabidopsis uncovered their functions in the development of both vegetative and reproductive organs. Conclusions Petunia genome includes 11 ALOG genes that can be divided into eight distinct groups, and they also show different expression patterns. Among these genes, PhLSH7b and PhLSH7a play significant roles in plant growth and development, especially in fruit development. Our results provide new insight into the evolution of ALOG gene family and have laid a good foundation for the study of petunia LSH gene in the future.

scholarly journals Genome-wide identification and expression analysis of sucrose nonfermenting-1-related protein kinase (SnRK) genes in Triticum aestivum in response to abiotic stress

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shefali Mishra ◽  
Pradeep Sharma ◽  
Rajender Singh ◽  
Ratan Tiwari ◽  
Gyanendra Pratap Singh
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Phylogenetic Analyses ◽  
Abiotic Stress Tolerance ◽  
Functional Characterization ◽  
Protein Motif ◽  
Element Analysis ◽  
Genome Wide ◽  
A Genome

AbstractThe SnRK gene family is a key regulator that plays an important role in plant stress response by phosphorylating the target protein to regulate subsequent signaling pathways. This study was aimed to perform a genome-wide analysis of the SnRK gene family in wheat and the expression profiling of SnRKs in response to abiotic stresses. An in silico analysis identified 174 SnRK genes, which were then categorized into three subgroups (SnRK1/2/3) on the basis of phylogenetic analyses and domain types. The gene intron–exon structure and protein-motif composition of SnRKs were similar within each subgroup but different amongst the groups. Gene duplication and synteny between the wheat and Arabidopsis genomes was also investigated in order to get insight into the evolutionary aspects of the TaSnRK family genes. The result of cis-acting element analysis showed that there were abundant stress- and hormone-related cis-elements in the promoter regions of 129 SnRK genes. Furthermore, quantitative real-time PCR data revealed that heat, salt and drought treatments enhanced TaSnRK2.11 expression, suggesting that it might be a candidate gene for abiotic stress tolerance. We also identified eight microRNAs targeting 16 TaSnRK genes which are playing important role across abiotic stresses and regulation in different pathways. These findings will aid in the functional characterization of TaSnRK genes for further research.

scholarly journals Genome-Wide Identification and Expression Profiling Analysis of Wnt Family Genes Affecting Adipocyte Differentiation in Cattle

2021 ◽  
Author(s):  
Cuili Pan ◽  
Shuzhe Wang ◽  
Chaoyun Yang ◽  
Chunli Hu ◽  
Hui Sheng ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Protein Motif ◽  
Chromosomal Distribution ◽  
Specific Expression ◽  
Wnt Proteins ◽  
Genome Wide ◽  
Protein Properties ◽  
Bovine Adipocytes

Abstract Wnt is a family of conserved glycoproteins that functions in a variety of crucial biological processes including tissue regeneration, animal development, and cell proliferation and differentiation. For its functional diversity and importance, Wnt gene family has gained considerable research interest in a variety of species. However, comprehensive identification and analysis of Wnt genes in Bovinae is lacking. In this study, we identified the repertoire of Wnt genes in cattle and seven other species of Bovinae and obtained 19 Wnt genes. Protein properties of these Wnt genes were also described. Phylogenetic analysis showed that the 149 Wnt proteins in Bovinae, together with 38 Wnt proteins from human and mouse, were clustered into 12 major clades. The Wnt genes belonging to the same subfamilies shared similar protein motif compositions and exon-intron patterns. Chromosomal distribution and collinearity analysis of Wnt genes among cattle and five species of Bovinae revealed that this gene family was conservative in evolution. RNA-seq data analysis indicated that Wnt genes exhibited tissue-specific expression patterns in cattle. qPCR analysis of Wnt gene family showed that each gene had a unique expression pattern during bovine adipocytes differentiation. And the comprehensive analysis indicated that Wnt2B may regulate adipose differentiation through activation of FZD5, which is worthy of further study. Our study presents the first genome-wide study of Wnt gene family in Bovinae, and lay the foundation for further functional characterization of the Wnt family in bovine adipocytes differentiation.

scholarly journals Genome-wide identification and functional characterization of Camelina sativa WRKY gene family in response to abiotic stress

2020 ◽  
Author(s):  
Yanan Song ◽  
Hongli Cui ◽  
Ying Shi ◽  
Jinai Xue ◽  
Chunli Ji ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Stress Resistance ◽  
Segmental Duplication ◽  
Functional Characterization ◽  
High Stress ◽  
Camelina Sativa ◽  
Genome Wide ◽  
Large Expansion

Abstract Background: WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, knowledge is limited for WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance against various stresses. Here, genome-wide characterization of WRKY proteins is performed to examine their gene-structures, phylogenetics, expressions, conserved motif organizations, and functional annotation to identify candidate WRKYs mediating regulation of stress resistance in camelina.Results: Total of 242 CsWRKY proteins encoded by 224 gene loci distributed uneven on chromosomes were identified, and classified into three groups via phylogenetic analysis according to their WRKY domains and zinc finger motifs. 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in C. sativa and Arabidopsis genomes as well as 282 pairs for C. sativa and B. napus, respectively. 137 segmental duplication events were observed but no tandem duplication in camelina genome. Ten major conserved motifs were examined, with WRKYGQK as the most conserved and several variants existed in many CsWRKYs. Expression analysis revealed that half more CsWRKY genes were expressed constitutively, and a set of them had a tissue-specific expression. Notably, 11 CsWRKY genes exhibited significantly expression changes in plant seedlings under cold, salt, and drought stress, respectively, having preferentially inducible expression pattern in response to the stress.Conclusions: The present described a detail analysis of CsWRKY gen family and their expression profiled in twelve tissues and under several stress conditions. Segmental duplication is the major force for large expansion of this gene family, and a strong purifying pressure happened for CsWRKY proteins evolutionally. CsWRKY proteins play important roles for plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms were found to be the key players possibly in mediating plant response to various stresses. Overall, our results provide a foundation for understanding roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance to stress as well as development of stress tolerance cultivars for Cruciferae crops.

scholarly journals Genome-Wide Identification and Analysis of VQ Motif-containing Gene Family in Brassica napus and Functional Characterization of BnMKS1 in Response to Leptosphaeria maculans

2020 ◽  
Author(s):  
Zhongwei Zou ◽  
Fei Liu ◽  
Shuanglong Huang ◽  
DILANTHA GERARD FERNANDO
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Functional Characterization ◽  
Leptosphaeria Maculans ◽  
Defense Responses ◽  
Marker Genes ◽  
Blackleg Disease ◽  
Genome Wide ◽  
A Genome

Proteins containing Valine-glutamine (VQ) motifs play important roles in plant growth and development, as well as in defense responses to both abiotic and biotic stresses. Blackleg disease, which is caused by Leptosphaeria maculans, is the most important disease in canola (Brassica napus L.) worldwide. H; however, the identification of B. napus VQs and their functions in response to blackleg disease have not yet been reported. In this study, we conducted a genome genome-wide identification and characterization of the VQ gene family in B. napus, including chromosome location, phylogenetic relations, gene structure, motif domain, synteny analysis, and cis-elements categorization of their promoter regions. To understand B. napus VQ gene function in response to blackleg disease, we overexpressed BnVQ7 (BnaA01g36880D, also known as the mitogen-activated protein kinase4 substrate1 (MKS1) gene) in a blackleg-susceptible canola variety Westar. Overexpression The overexpression of BnMKS1 in canola did not improve its resistance to blackleg disease at the seedling stage. H; however, transgenic canola plants overexpressing BnMKS1 displayed an enhanced resistance to L. maculans infection at the adult plant stage. Expression levels of downstream and defense marker genes in cotyledons increased significantly at the necrotrophic stage of L. maculans infection in the overexpression line of BnMKS1, suggesting that the SA salicylic acid (SA)- and jasmonic acid (JA )-mediated signaling pathways were both involved in the defense responses. Together, these results suggest that BnMKS1 might play an important role in the defense against L. maculans.

scholarly journals Genome-wide identification, phylogeny, and expression profile of the sucrose transporter multigene family in tobacco

2019 ◽  
Vol 99 (3) ◽  
pp. 312-323
Author(s):  
Shanshan Wang ◽  
Jun Yang ◽  
Xiaodong Xie ◽  
Feng Li ◽  
Mingzhu Wu ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Functional Characterization ◽  
Nicotiana Sylvestris ◽  
Multiple Roles ◽  
Functional Conservation ◽  
Sucrose Transporters ◽  
Genome Wide ◽  
Pi Starvation ◽  
Profiling Analysis

The transportation and distribution of sucrose in plants is mediated by sucrose transporters (SUTs), which also participate in various plant developmental and resistance processes. However, no such study of the tobacco SUT family has been reported yet. In the present study, 11, 5, and 4 SUT genes were identified from the genomes of Nicotiana tabacum, Nicotiana sylvestris, and Nicotiana tomentosiformis, respectively. The exon–intron structures of the tobacco SUT genes were highly conserved in the three tobacco species. Gene loss, duplication, and chromosome exchange occurred in the NtSUT family during the formation of allotetraploid common tobacco. Expression profiling analysis revealed that the expression patterns of the NtSUT genes in common tobacco were closer to those in N. sylvestris plants. The NtSUT2s and NtSUT4 genes were ubiquitously expressed in various tobacco tissues, while the NtSUT1s gene was highly expressed in the maturing leaves, indicating their functional conservation and differentiation. The transcriptions of the NtSUT2t, NtSUT3s, NtSUT4, and NtSUT5s genes in tobacco plants were dramatically induced under Pi starvation, drought, and salinity stresses, but their highest expression levels occurred in different tissues, suggesting the multiple roles of NtSUTs in plant resistance to various abiotic stresses. This study provides useful information for the further functional characterization of SUT genes in tobacco.

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