Genome-scale identification of plant defensin (PDF) family genes and molecular characterization of their responses to diverse nutrient stresses in allotetraploid rapeseed

Plant defensins (PDFs), short peptides with strong antibacterial activity, play important roles in plant growth, development, and stress resistance. However, there are few systematic analyses on PDFs in Brassica napus. Here, bioinformatics methods were used to identify genome-wide PDFs in Brassica napus, and systematically analyze physicochemical properties, expansion pattern, phylogeny, and expression profiling of BnaPDFs under diverse nutrient stresses. A total of 37 full-length PDF homologs, divided into two subgroups (PDF1s and PDF2s), were identified in the rapeseed genome. A total of two distinct clades were identified in the BnaPDF phylogeny. Clade specific conserved motifs were identified within each clade respectively. Most BnaPDFs were proved to undergo powerful purified selection. The PDF members had enriched cis-elements related to growth and development, hormone response, environmental stress response in their promoter regions. GO annotations indicate that the functional pathways of BnaPDFs are mainly involved in cells killing and plant defense responses. In addition, bna-miRNA164 and bna-miRNA172 respectively regulate the expression of their targets BnaA2.PDF2.5 and BnaC7.PDF2.6. The expression patterns of BnaPDFs were analyzed in different tissues. BnaPDF1.2bs was mainly expressed in the roots, whereas BnaPDF2.2s and BnaPDF2.3s were both expressed in stamen, pericarp, silique, and stem. However, the other BnaPDF members showed low expression levels in various tissues. Differential expression of BnaPDFs under nitrate limitation, ammonium excess, phosphorus starvation, potassium deficiency, cadmium toxicity, and salt stress indicated that they might participate in different nutrient stress resistance. The genome-wide identification and characterization of BnaPDFs will enrich understanding of their molecular characteristics and provide elite gene resources for genetic improvement of rapeseed resistance to nutrient stresses.

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

Phytopathology ◽

10.1094/phyto-04-20-0134-r ◽

2020 ◽

Cited By ~ 1

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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Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus

BMC Plant Biology ◽

10.1186/s12870-020-02752-2 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Weizhuo Zhu ◽

Yiyi Guo ◽

Yeke Chen ◽

Dezhi Wu ◽

Lixi Jiang

Keyword(s):

Brassica Napus ◽

Stress Condition ◽

Expression Patterns ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Good Opportunity ◽

Domain Structures ◽

Genome Wide ◽

A Genome

Abstract Background Transcription factors GATAs are involved in plant developmental processes and respond to environmental stresses through binding DNA regulatory regions to regulate their downstream genes. However, little information on the GATA genes in Brassica napus is available. The release of the reference genome of B. napus provides a good opportunity to perform a genome-wide characterization of GATA family genes in rapeseed. Results In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus, which were classified into four subfamilies based on phylogenetic analysis and their domain structures. The amino acids of BnGATAs were obvious divergence among four subfamilies in terms of their GATA domains, structures and motif compositions. Gene duplication and synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distributions of BnGATAs in a core collection germplasm are probably associated with functional disparity under environmental stress condition in different genotypes of B. napus. Conclusion The present study was investigated genomic structures, evolution features, expression patterns and SNP distributions of 96 BnGATAs. The results enrich our understanding of the GATA genes in rapeseed.

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

10.21203/rs.3.rs-17109/v1 ◽

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.

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Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus

10.21203/rs.3.rs-30607/v3 ◽

2020 ◽

Author(s):

Weizhuo Zhu ◽

Yiyi Guo ◽

Yeke Chen ◽

Dezhi Wu ◽

Lixi Jiang

Keyword(s):

Brassica Napus ◽

Stress Condition ◽

Expression Patterns ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Good Opportunity ◽

Domain Structures ◽

Genome Wide ◽

A Genome

Abstract Background: Transcription factors GATAs are involved in plant developmental processes and respond to environmental stresses through binding DNA regulatory regions to regulate their downstream genes. However, little information on the GATA genes in Brassica napus is available. The release of the reference genome of B. napus provides a good opportunity to perform a genome-wide characterization of GATA family genes in rapeseed.Results: In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus, which were classified into four subfamilies based on phylogenetic analysis and their domain structures. The amino acids of BnGATAs were obvious divergence among four subfamilies in terms of their GATA domains, structures and motif compositions. Gene duplication and synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distributions of BnGATAs in a core collection germplasm are probably associated with functional disparity under environmental stress condition in different genotypes of B. napus.Conclusion: The present study was investigated genomic structures, evolution features, expression patterns and SNP distributions of 96 BnGATAs. The results enrich our understanding of the GATA genes in rapeseed.

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Genome-wide identification, characterization and expression analysis of BES1 gene family in tomato

BMC Plant Biology ◽

10.1186/s12870-021-02933-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Deding Su ◽

Wei Xiang ◽

Ling Wen ◽

Wang Lu ◽

Yuan Shi ◽

...

Keyword(s):

Target Genes ◽

Expression Patterns ◽

Transcriptional Repressors ◽

Promoter Regions ◽

Specific Expression ◽

Genome Wide ◽

Development Processes ◽

Genomic Characterization ◽

Functional Features

Abstract Background As the key regulators in BR signaling, BES1 family genes regulate thousands of target genes involved in various development processes. So far, the functions of BES1 family are poorly understood in tomato, and a comprehensive genomic and expressional analysis is worth to conduct for this family. Results Here, nine SlBES1 family members were identified in tomato and classified into five groups based on the conserved motif, gene structure and phylogenetic analysis. Synteny among tomato, Arabidopsis, pepper and rice were further analyzed to obtain insights into evolutionary characteristics. Several cis-elements related to hormone, stress and plant development were exhibited in the promoter regions of SlBES1 family genes. Subcellular localization showed seven members localized both in the nucleus and cytoplasm, implying the presence of dephosphorylated and phosphorylated form of these seven proteins, furthermore, five of them possessed transcription activation activity whereas the left two functioned as transcriptional repressors. Another two members, however, neither localized in the nucleus nor had transactivation activity. Besides, SlBES1.8 showed flower-specific expression while other members expressed ubiquitously in all organs. Moreover, SlBES1 genes exhibited variational expression in response to nine principal plant hormones. Notably, the expression levels of SlBES1 genes presented a dominant downregulated trend in response to stresses. Conclusions In this study, we systematically analyzed the genomic characterization of SlBES1 family, together with the analyses of protein functional features and expression patterns, our results lay a foundation for the functional research of SlBES1 family.

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Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus

10.21203/rs.3.rs-30607/v2 ◽

2020 ◽

Author(s):

Weizhuo Zhu ◽

Yiyi Guo ◽

Yeke Chen ◽

Dezhi Wu ◽

Lixi Jiang

Keyword(s):

Brassica Napus ◽

Stress Condition ◽

Expression Patterns ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Good Opportunity ◽

Domain Structures ◽

Genome Wide ◽

A Genome

Abstract Background: Transcription factors GATAs are involved in plant developmental processes and respond to environmental stresses through binding DNA regulatory regions to regulate their downstream genes. However, little information on the GATA genes in Brassica napus is available. The release of the reference genome of B. napus provides a good opportunity to perform a genome-wide characterization of GATA family genes in rapeseed. Results: In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus , which were classified into four subfamilies based on phylogenetic analysis and their domain structures. The amino acids of BnGATAs were obvious divergence among four subfamilies in terms of their GATA domains, structures and motif compositions. Gene duplication and synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distributions of BnGATAs in a core collection germplasm are probably associated with functional disparity under environmental stress condition in different genotypes of B. napus . Conclusion: The present study was investigated genomic structures, evolution features, expression patterns and SNP distributions of 96 BnGATAs. The results enrich our understanding of the GATA genes in rapeseed.

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Genome-Wide Identification and Analysis of Polygalacturonase Genes in Solanum lycopersicum

International Journal of Molecular Sciences ◽

10.3390/ijms19082290 ◽

2018 ◽

Vol 19 (8) ◽

pp. 2290 ◽

Cited By ~ 11

Author(s):

Xubo Ke ◽

Huasen Wang ◽

Yang Li ◽

Biao Zhu ◽

Yunxiang Zang ◽

...

Keyword(s):

Solanum Lycopersicum ◽

Expression Profiles ◽

Expression Patterns ◽

Amino Acid Sequences ◽

Evolutionary Analysis ◽

Environmental Stress Response ◽

Promoter Regions ◽

Genome Wide ◽

Specific Organ ◽

Organ Tissue

Polygalacturonase (PG), a large hydrolase family in plants, is involved in pectin disassembly of the cell wall in plants. The present study aims to characterize PG genes and investigate their expression patterns in Solanum lycopersicum. We identified 54 PG genes in the tomato genome and compared their amino acid sequences with their Arabidopsis counterpart. Subsequently, we renamed these PG genes according to their Arabidopsis homologs. Phylogenetic and evolutionary analysis revealed that these tomato PG genes could be classified into seven clades, and within each clade the exon/intron structures were conserved. Expression profiles analysis through quantitive real-time polymerase chain reaction (qRT-PCR) revealed that most SlPGs had specific or high expression patterns in at least one organ, and particularly five PG genes (SlPG14, SlPG15, SlPG49, SlPG70, and SlPG71) associated with fruit development. Promoter analysis showed that more than three cis-elements associated with plant hormone response, environmental stress response or specific organ/tissue development exhibited in each SlPG promoter regions. In conclusion, our results may provide new insights for the further study of PG gene function during plant development.

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Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors

PeerJ ◽

10.7717/peerj.7511 ◽

2019 ◽

Vol 7 ◽

pp. e7511 ◽

Cited By ~ 1

Author(s):

Ziwei Liang ◽

Mengdi Li ◽

Zhengyi Liu ◽

Jianbo Wang

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Expression Patterns ◽

Brassica Napus L ◽

Genome Wide ◽

Domain Loss ◽

As Stress ◽

Evolution Of Proteins ◽

Genome Triplication

Heat shock protein 70 (Hsp70) plays an essential role in plant growth and development, as well as stress response. Rapeseed (Brassica napus L.) originated from recently interspecific hybridization between Brassica rapa and Brassica oleracea. In this study, a total of 47 Hsp70 genes were identified in B. napus (AnAnCnCn genome), including 22 genes from An subgenome and 25 genes from Cn subgenome. Meanwhile, 29 and 20 Hsp70 genes were explored in B. rapa (ArAr genome) and B. oleracea (CoCo genome), respectively. Based on phylogenetic analysis, 114 Hsp70 proteins derived from B. napus, B. rapa, B. oleracea and Arabidopsis thaliana, were divided into 6 subfamilies containing 16 Ar-An and 11 Co-Cn reliable orthologous pairs. The homology and synteny analysis indicated whole genome triplication and segmental duplication may be the major contributor for the expansion of Hsp70 gene family. Intron gain of BnHsp70 genes and domain loss of BnHsp70 proteins also were found in B. napus, associating with intron evolution and module evolution of proteins after allopolyploidization. In addition, transcriptional profiles analyses indicated that expression patterns of most BnHsp70 genes were tissue-specific. Moreover, Hsp70 orthologs exhibited different expression patterns in the same tissue and Cn subgenome biased expression was observed in leaf. These findings contribute to exploration of the evolutionary adaptation of polyploidy and will facilitate further application of BnHsp70 gene functions.

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

10.21203/rs.3.rs-17109/v2 ◽

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

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

Genome ◽

10.1139/gen-2018-0161 ◽

2019 ◽

Vol 62 (9) ◽

pp. 597-608 ◽

Cited By ~ 2

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.

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