scholarly journals Genome-wide identification and characterization of SnRK family genes in Brassica napus

2020 ◽  
Author(s):  
Weizhuo Zhu ◽  
Dezhi Wu ◽  
Lixi Jiang ◽  
Lingzhen Ye
Keyword(s):  
Brassica Napus ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Composition Analysis ◽  
Distribution Analysis ◽  
Element Analysis ◽  
Genome Wide ◽  
Identification And Characterization

Abstract Background: Sucrose non-fermenting 1 related protein kinases (SnRK) play crucial roles in responding to biotic and abiotic stresses through activating protein phosphorylation pathways. However, little information of SnRK genes was available in Brassica napus, one of important oil crops. Recently, the released sequences of the reference genome of B.napus provide a good chance to perform genome-wide identification and characterization of BnSnRK gene family in the rapeseed.Results: Totally 114 SnRK genes distributed on 19 chromosomes were identified in the genome of B.napus and classified into three subfamilies on the basis of phylogenetic analysis and the domain types. According to gene structure and motif composition analysis, the BnSnRK sequences showed obvious divergence among three subfamilies. Gene duplication and synteny between the genomes of the rapeseed and Arabidopsis were also analyzed to provide insights into the evolutionary characteristics of BnSnRK family genes. Cis-element analysis revealed that BnSnRKs may response to diverse environmental stresses. Moreover, the expression patterns of BnSnRKs in various tissues and under diverse abiotic stresses were distinct difference. Besides, Single Nucleotide Polymorphisms (SNP) distribution analysis suggests the function disparity of BnSnRK family genes in different genotypes of the rapeseed.Conclusion: We examined genomic structures, evolution features, expression patterns and SNP distribution of 114 BnSnRKs. The results provide valuable information for functional characterization of BnSnRK genes in future studies.

scholarly journals Genome-wide identification and characterization of SnRK family genes in Brassica napus

2020 ◽  
Author(s):  
Weizhuo Zhu ◽  
Dezhi Wu ◽  
Lixi Jiang ◽  
Lingzhen Ye
Keyword(s):  
Brassica Napus ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Composition Analysis ◽  
Distribution Analysis ◽  
Element Analysis ◽  
Genome Wide ◽  
Identification And Characterization

Abstract Background: Sucrose non-fermenting 1 related protein kinases (SnRK) play crucial roles in responding to biotic and abiotic stresses through activating protein phosphorylation pathways. However, little information of SnRK genes was available in Brassica napus, one of important oil crops. Recently, the released sequences of the reference genome of B.napus provide a good chance to perform genome-wide identification and characterization of BnSnRK gene family in the rapeseed.Results: Totally 114 SnRK genes distributed on 19 chromosomes were identified in the genome of B.napus and classified into three subfamilies on the basis of phylogenetic analysis and the domain types. According to gene structure and motif composition analysis, the BnSnRK sequences showed obvious divergence among three subfamilies. Gene duplication and synteny between the genomes of the rapeseed and Arabidopsis were also analyzed to provide insights into the evolutionary characteristics of BnSnRK family genes. Cis-element analysis revealed that BnSnRKs may response to diverse environmental stresses. Moreover, the expression patterns of BnSnRKs in various tissues and under diverse abiotic stresses were distinct difference. Besides, Single Nucleotide Polymorphisms (SNP) distribution analysis suggests the function disparity of BnSnRK family genes in different genotypes of the rapeseed.Conclusion: We examined genomic structures, evolution features, expression patterns and SNP distribution of 114 BnSnRKs. The results provide valuable information for functional characterization of BnSnRK genes in future studies.

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.

Genome-wide identification and characterization of Gretchen Hagen3 (GH3) family genes in Brassica napus

Genome ◽  
2019 ◽  
Vol 62 (9) ◽  
pp. 597-608 ◽  
Author(s):  
Lijuan Wei ◽  
Bo Yang ◽  
Hongju Jian ◽  
Aoxiang Zhang ◽  
Ruiying Liu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Oilseed Rape ◽  
Expression Patterns ◽  
Gene Families ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Gene Structures ◽  
Identification And Characterization ◽  
Exogenous Iaa

The hormone auxin is involved in many biological processes throughout a plant’s lifecycle. However, genes in the GH3 (Gretchen Hagen3) family, one of the three major auxin-responsive gene families, have not yet been identified in oilseed rape (Brassica napus). In this study, we identified 63 BnaGH3 genes in oilseed rape using homology searches. We analyzed the chromosome locations, gene structures, and phylogenetic relationships of the BnaGH3 genes, as well as the cis-elements in their promoters. Most BnaGH3 genes are located on chromosomes A03, A09, C02, C03, and C09, each with 4–7 members. In addition, we analyzed the expression patterns of BnaGH3 genes in seven tissues by transcriptome sequencing and quantitative RT-PCR analysis of plants under exogenous IAA treatment. The BnaGH3 genes showed different expression patterns in various tissues. BnaA.GH3.2-1 and BnaC.GH3.2-1 were expressed in the seed and seed coat during development and in response to IAA treatment. These results shed light on the possible roles of the GH3 gene family in oilseed rape.

scholarly journals Genome-Wide Identification and Characterization of FBA Gene Family in Polyploid Crop Brassica napus

2019 ◽  
Vol 20 (22) ◽  
pp. 5749 ◽  
Author(s):  
Zhao ◽  
Liu ◽  
Zhang ◽  
Hu ◽  
Liu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Calvin Cycle ◽  
Regulatory Elements ◽  
Metabolic Enzyme ◽  
Genome Wide ◽  
Identification And Characterization

Fructose-1,6-bisphosphate aldolase (FBA) is a versatile metabolic enzyme involved in multiple important processes of glycolysis, gluconeogenesis, and Calvin cycle. Despite its significance in plant biology, the identity of this gene family in oil crops is lacking. Here, we performed genome-wide identification and characterization of FBAs in an allotetraploid species, oilseed rape Brassica napus. Twenty-two BnaFBA genes were identified and divided into two groups based on integrative analyses of functional domains, phylogenetic relationships, and gene structures. Twelve and ten B. napus FBAs (BnaFBAs) were predicted to be localized in the chloroplast and cytoplasm, respectively. Notably, synteny analysis revealed that Brassica-specific triplication contributed to the expansion of the BnaFBA gene family during the evolution of B. napus. Various cis-acting regulatory elements pertinent to abiotic and biotic stresses, as well as phytohormone responses, were detected. Intriguingly, each of the BnaFBA genes exhibited distinct sequence polymorphisms. Among them, six contained signatures of selection, likely having experienced breeding selection during adaptation and domestication. Importantly, BnaFBAs showed diverse expression patterns at different developmental stages and were preferentially highly expressed in photosynthetic tissues. Our data thus provided the foundation for further elucidating the functional roles of individual BnaFBA and also potential targets for engineering to improve photosynthetic productivity in B. napus.

scholarly journals Genome-Wide Identification and Characterization of GATA Family Genes in Brassica Napus

2020 ◽  
Author(s):  
Weizhuo Zhu ◽  
Yiyi Guo ◽  
Yeke Chen ◽  
Dezhi Wu ◽  
Lixi Jiang
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Distribution Analysis ◽  
Nucleotide Polymorphisms ◽  
Good Opportunity ◽  
Domain Structures ◽  
Oil Crops ◽  
Genome Wide ◽  
A Genome

Abstract Background: GATA transcription factors are involved in plant developmental processes, which also respond to environmental stresses through binding DNA regulatory regions to regulate the downstream genes. However, little information of GATA genes is available in Brassica napus, one of important oil crops. The release of B. napus genome sequences provides a good opportunity to perform a genome-wide characterization of GATA family genes in the rapeseed genome. Results: In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus. They were classified into four subfamilies on the basis of phylogenetic analysis and the domain structures. The sequences of BnGATAs were obvious divergence among four subfamilies based on their GATA domains, structures and motif compositions. Gene duplication and the synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into the evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distribution analysis suggests functional disparity of GATA family genes in different genotypes of a core collection germplasm.Conclusion: This study examined genomic structures, evolution features, expression patterns and SNP distribution of 96 BnGATAs. The results enriched our knowledge of the GATA genes in rapeseed.

scholarly journals Identification and Characterization of Abiotic Stress Responsive CBL-CIPK Family Genes in Medicago

2021 ◽  
Vol 22 (9) ◽  
pp. 4634
Author(s):  
Wenxuan Du ◽  
Junfeng Yang ◽  
Lin Ma ◽  
Qian Su ◽  
Yongzhen Pang
Keyword(s):  
Abiotic Stress ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Interacting Protein ◽  
Forage Crop ◽  
Cis Acting ◽  
Protein Motifs ◽  
Plant Signal Transduction ◽  
Identification And Characterization

The calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) play important roles in plant signal transduction and response to abiotic stress. Plants of Medicago genus contain many important forages, and their growth is often affected by a variety of abiotic stresses. However, studies on the CBL and CIPK family member and their function are rare in Medicago. In this study, a total of 23 CBL and 58 CIPK genes were identified from the genome of Medicago sativa as an important forage crop, and Medicaog truncatula as the model plant. Phylogenetic analysis suggested that these CBL and CIPK genes could be classified into five and seven groups, respectively. Moreover, these genes/proteins showed diverse exon-intron organizations, architectures of conserved protein motifs. Many stress-related cis-acting elements were found in their promoter region. In addition, transcriptional analyses showed that these CBL and CIPK genes exhibited distinct expression patterns in various tissues, and in response to drought, salt, and abscisic acid treatments. In particular, the expression levels of MtCIPK2 (MsCIPK3), MtCIPK17 (MsCIPK11), and MtCIPK18 (MsCIPK12) were significantly increased under PEG, NaCl, and ABA treatments. Collectively, our study suggested that CBL and CIPK genes play crucial roles in response to various abiotic stresses in Medicago.

scholarly journals Genome wide identification and characterization of light-harvesting Chloro a/b binding (LHC) genes reveals their potential role in enhancing drought tolerance in Gossypium hirsutum

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Teame Gereziher MEHARI ◽  
Yanchao XU ◽  
Richard Odongo MAGWANGA ◽  
Muhammad Jawad UMER ◽  
Joy Nyangasi KIRUNGU ◽  
...  
Keyword(s):  
Drought Stress ◽  
Gossypium Hirsutum ◽  
Abiotic Stresses ◽  
Substitution Rate ◽  
Synonymous Substitution ◽  
Synonymous Substitution Rate ◽  
Drought Tolerant ◽  
Genome Wide ◽  
Identification And Characterization

Abstract Background Cotton is an important commercial crop for being a valuable source of natural fiber. Its production has undergone a sharp decline because of abiotic stresses, etc. Drought is one of the major abiotic stress causing significant yield losses in cotton. However, plants have evolved self-defense mechanisms to cope abiotic factors like drought, salt, cold, etc. The evolution of stress responsive transcription factors such as the trihelix, a nodule-inception-like protein (NLP), and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic stresses. Results Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding (LHC) genes were carried out in cotton under drought stress conditions. A hundred and nine proteins encoded by the LHC genes were found in the cotton genome, with 55, 27, and 27 genes found to be distributed in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. The proteins encoded by the genes were unevenly distributed on various chromosomes. The Ka/Ks (Non-synonymous substitution rate/Synonymous substitution rate) values were less than one, an indication of negative selection of the gene family. Differential expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem tissues. Most genes were found to be highly expressed in MR-85, a relative drought tolerant germplasm. Conclusion The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance, and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.

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.

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