scholarly journals Genome-wide Survey of the bHLH Super Gene Family in Brassica napus

2020 ◽  
Author(s):  
Yunzhuo Ke ◽  
Yunwen Wu ◽  
Hongjun Zhou ◽  
Ping Chen ◽  
Mangmang Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Root Development ◽  
Expression Profiles ◽  
Joint Analysis ◽  
Sequence Motifs ◽  
Intron Insertion ◽  
Helix Loop Helix ◽  
Genome Wide ◽  
Organization Analysis

Abstract Background: The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop, Brassica napus. Results: We identified 602 potential bHLHs in the B. napus genome (BnabHLHs) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions of BnabHLHs. Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnabHLHs. Expression analyses showed that BnabHLHs were widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects of B. napus development. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA3, gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles of BnabHLHs changed significantly, with many showing increased expression. The induction of five candidate BnabHLHs was confirmed following the five hormone treatments via qRT-PCR. Up to 246 BnabHLHs from nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function. Conclusion: The 602 BnabHLHs identified from B. napus were classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development in B. napus. Moreover, this study provides important insights into the potential functions of the BnabHLHs super gene family and thus will be useful in future gene function research.

Genome-wide Survey of the bHLH Super Gene Family in Brassica napus and its Role in Roots

2020 ◽  
Author(s):  
Yunzhuo Ke ◽  
Yunwen Wu ◽  
Hongjun Zhou ◽  
Ping Chen ◽  
Mangmang Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Root Development ◽  
Expression Profiles ◽  
Joint Analysis ◽  
Sequence Motifs ◽  
Intron Insertion ◽  
Helix Loop Helix ◽  
Genome Wide ◽  
Organization Analysis

Abstract Background: The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop, Brassica napus. Results: We identified 602 potential bHLHs in the B. napus genome (BnabHLHs) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions of BnabHLHs. Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnabHLHs. Expression analyses showed that BnabHLHs were widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects of B. napus development. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA3, gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles of BnabHLHs changed significantly, with many showing increased expression. The induction of five candidate BnabHLHs was confirmed following the five hormone treatments via qRT-PCR. Up to 246 BnabHLHs from nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function. Conclusion: The 602 BnabHLHs identified from B. napus were classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development in B. napus. Moreover, this study provides important insights into the potential functions of the BnabHLHs super gene family and thus will be useful in future gene function research.

scholarly journals Genome-wide Survey of the bHLH Super Gene Family in Brassica napus

2020 ◽  
Author(s):  
Yunzhuo Ke ◽  
Yunwen Wu ◽  
Hongjun Zhou ◽  
Ping Chen ◽  
Mangmang Wang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Brassica Napus ◽  
Gene Family ◽  
Root Development ◽  
Expression Profiles ◽  
Joint Analysis ◽  
Bhlh Transcription Factor ◽  
Sequence Motifs ◽  
Intron Insertion ◽  
Helix Loop Helix

Abstract Background: The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop, Brassica napus . Results : We identified 602 potential bHLHs in the B. napus genome ( BnabHLHs ) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions of BnabHLHs . Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnabHLHs . Expression analyses showed that BnabHLHs were widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects of B. napus development. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA 3 , gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles of BnabHLHs changed significantly, with many showing increased expression. The induction of five candidate BnabHLHs was confirmed following the five hormone treatments via qRT-PCR. Up to 246 BnabHLHs from nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function. Conclusion: The 602 BnabHLHs identified from B. napus were classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development in B. napus . Moreover, this study provides important insights into the potential functions of the BnabHLHs super gene family and thus will be useful in future gene function research. Keywords: Brassica napus ; bHLH transcription factor; root; gene expression

Genome-wide Survey of bHLH Super Gene Family in Brassica napus and Their Roles in Roots

2019 ◽  
Author(s):  
Yunzhuo Ke ◽  
Yunwen Wu ◽  
Hongjun Zhou ◽  
Ping Chen ◽  
Mangmang Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Expression Profiles ◽  
Joint Analysis ◽  
Pcr Analysis ◽  
Sequence Motifs ◽  
Intron Insertion ◽  
Under Five ◽  
Helix Loop Helix ◽  
Root Hair Development

Abstract Background: Basic helix-loop-helix (bHLH) gene family is one of the largest transcription factors in plants and are functionally characterized in diverse species. However, less is known about their functions in the economically important allopolyploid oil crop, Brassica napus . Results : We identified 602 potential bHLHs in B. napus genome ( BnbHLHs ) and categorized them into 36 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure and exon-intron organization analysis. The intron insertion patterns of this gene family were corrected and a total of eight types were identified in the bHLH regions of BnbHLHs . Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnbHLHs . Expression analyses showed that BnbHLHs were wide and formed six main patterns, suggesting they may participate in various aspects in B. napus during the development. The expression profiles under five hormone treatments (IAA, ABA, ACC, GA3, 6-BA) in roots further revealed the active response of BnbHLHs with a large proportion of which being induced. qRT-PCR analysis confirmed the expression profiles of five candidate BnbHLHs under five hormone inductions. Up to 246 BnbHLHs from nine subfamilies were predicted to have potential roles relating to root development by joint analysis of expression profile and homolog function. Further, the MYB/bHLH/WD40 (MBW) protein complex regulating root hair development were verified in B. napus by yeast two-hybrid experiment. Conclusion: The 602 BnbHLHs identified from B. napus could be classed into 36 subfamilies, and those members from the same subfamily generally have similar sequence motifs. BnbHLHs may widely involve in root biological process in B. napus . Overall, this study provides important insights into the characterization and potential functions of B. napus bHLH super gene family and thus will be useful in future gene function research.

scholarly journals Genome-wide survey and expression analyses of the GRAS gene family in Brassica napus reveals their roles in root development and stress response

Planta ◽  
2019 ◽  
Vol 250 (4) ◽  
pp. 1051-1072 ◽  
Author(s):  
Pengcheng Guo ◽  
Jing Wen ◽  
Jin Yang ◽  
Yunzhuo Ke ◽  
Mangmang Wang ◽  
...  
Keyword(s):  
Stress Response ◽  
Brassica Napus ◽  
Gene Family ◽  
Root Development ◽  
Genome Wide ◽  
Genome Wide Survey ◽  
Gras Gene

scholarly journals Genome-wide analysis and expression patterns of lipid phospholipid phospholipase gene family in Brassica napus L.

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Su ◽  
Ali Raza ◽  
Liu Zeng ◽  
Ang Gao ◽  
Yan Lv ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Stress Conditions ◽  
Motif Analysis ◽  
Genome Wide Analysis ◽  
Group I ◽  
Genome Wide ◽  
A Genome

Abstract Background Lipid phosphate phosphatases (LPP) are critical for regulating the production and degradation of phosphatidic acid (PA), an essential signaling molecule under stress conditions. Thus far, the LPP family genes have not been reported in rapeseed (Brassica napus L.). Results In this study, a genome-wide analysis was carried out to identify LPP family genes in rapeseed that respond to different stress conditions. Eleven BnLPPs genes were identified in the rapeseed genome. Based on phylogenetic and synteny analysis, BnLPPs were classified into four groups (Group I-Group IV). Gene structure and conserved motif analysis showed that similar intron/exon and motifs patterns occur in the same group. By evaluating cis-elements in the promoters, we recognized six hormone- and seven stress-responsive elements. Further, six putative miRNAs were identified targeting three BnLPP genes. Gene ontology analysis disclosed that BnLPP genes were closely associated with phosphatase/hydrolase activity, membrane parts, phosphorus metabolic process, and dephosphorylation. The qRT-PCR based expression profiles of BnLPP genes varied in different tissues/organs. Likewise, several gene expression were significantly up-regulated under NaCl, PEG, cold, ABA, GA, IAA, and KT treatments. Conclusions This is the first report to describe the comprehensive genome-wide analysis of the rapeseed LPP gene family. We identified different phytohormones and abiotic stress-associated genes that could help in enlightening the plant tolerance against phytohormones and abiotic stresses. The findings unlocked new gaps for the functional verification of the BnLPP gene family during stresses, leading to rapeseed improvement.

scholarly journals The β- Amylase Gene Family in Brassica Napus: Genome Wide Analysis and Expression Profiles in Response to Abiotic Stresses

2020 ◽  
Author(s):  
Yan Lv ◽  
Dan Luo ◽  
Ziqi Jia ◽  
Yong Cheng ◽  
Xiling Zou
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Sequence Similarity ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Chromosomal Distribution ◽  
Brassica Crops ◽  
Genome Wide ◽  
Gene Structures

Abstract Background: The β amylase (BAM) gene family, known for their property of catalytic ability to hydrolyze starch to maltose units, has been recognized to play critical roles in metabolism and gene regulation. To date, BAM genes have not been characterized in oil crops.Results: In this study, the genome wide survey revealed the identification of 30 BnaBAM genes in Brassica napus (B. napus), 11 BraBAM genes in Brassica rapa (B. rapa), 20 BoBAM genes in Brassica oleracea (B. oleracea), which were divided into 4 subfamilies according to the sequence similarity and phylogenetic relationships. All the BAM genes identified in the allotetraploid genome of B. napus, as well as two parental related species (B. rapa and B. oleracea), were analyzed for the gene structures, chromosomal distribution and collinearity, the sequence alignment of the core glucosyl hydrolase domains was further applied. 30 BnaBAMs, 11 BraBAMs and 17 BoBAMs exhibited uneven distribution on chromosomes of Brassica crops. The similar structural compositions of BAM genes in the same subfamily suggested that they were relatively conserved. Abiotic stresses pose one of the major constraints to plant growth and productivity worldwide. Thus, the responsiveness of BnaBAM genes under abiotic stresses were analyzed in B. napus. The expression patterns revealed a stress responsive behavior of all members, of which BnaBAM3s were more prominent. These differential expression patterns suggested an intricate regulation of BnaBAMs elicited by environmental stimuli. Conclusion: Altogether, the present study provides first insights into the BAM gene family of Brassica crops, which lays the foundation for investigating the roles of stress--responsive BnaBAM candidates in B. napus.

scholarly journals Genome-Wide Analysis and Expression Profile of Superoxide Dismutase (SOD) Gene Family in Rapeseed (Brassica napus L.) under Different Hormones and Abiotic Stress Conditions

Antioxidants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1182
Author(s):  
Wei Su ◽  
Ali Raza ◽  
Ang Gao ◽  
Ziqi Jia ◽  
Yi Zhang ◽  
...  
Keyword(s):  
Superoxide Dismutase ◽  
Abiotic Stress ◽  
Brassica Napus ◽  
Gene Family ◽  
Expression Profiles ◽  
Protein Structures ◽  
Brassica Napus L ◽  
Genome Wide ◽  
A Genome ◽  
Sod Gene Family

Superoxide dismutase (SOD) is an important enzyme that acts as the first line of protection in the plant antioxidant defense system, involved in eliminating reactive oxygen species (ROS) under harsh environmental conditions. Nevertheless, the SOD gene family was yet to be reported in rapeseed (Brassica napus L.). Thus, a genome-wide investigation was carried out to identify the rapeseed SOD genes. The present study recognized 31 BnSOD genes in the rapeseed genome, including 14 BnCSDs, 11 BnFSDs, and six BnMSDs. Phylogenetic analysis revealed that SOD genes from rapeseed and other closely related plant species were clustered into three groups based on the binding domain with high bootstrap values. The systemic analysis exposed that BnSODs experienced segmental duplications. Gene structure and motif analysis specified that most of the BnSOD genes displayed a relatively well-maintained exon–intron and motif configuration within the same group. Moreover, we identified five hormones and four stress- and several light-responsive cis-elements in the promoters of BnSODs. Thirty putative bna-miRNAs from seven families were also predicted, targeting 13 BnSODs. Gene ontology annotation outcomes confirm the BnSODs role under different stress stimuli, cellular oxidant detoxification processes, metal ion binding activities, SOD activity, and different cellular components. Twelve BnSOD genes exhibited higher expression profiles in numerous developmental tissues, i.e., root, leaf, stem, and silique. The qRT-PCR based expression profiling showed that eight genes (BnCSD1, BnCSD3, BnCSD14, BnFSD4, BnFSD5, BnFSD6, BnMSD2, and BnMSD10) were significantly up-regulated under different hormones (ABA, GA, IAA, and KT) and abiotic stress (salinity, cold, waterlogging, and drought) treatments. The predicted 3D structures discovered comparable conserved BnSOD protein structures. In short, our findings deliver a foundation for additional functional investigations on the BnSOD genes in rapeseed breeding programs.

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 auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)

2017 ◽  
Vol 17 (1) ◽  
Author(s):  
Haitao Li ◽  
Bo Wang ◽  
Qinghua Zhang ◽  
Jing Wang ◽  
Graham J. King ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Indoleacetic Acid ◽  
Brassica Napus L ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

2022 ◽  
Vol 23 (2) ◽  
pp. 614
Author(s):  
Weiqi Sun ◽  
Mengdi Li ◽  
Jianbo Wang
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Gene Structure ◽  
Stress Responses ◽  
Stress Protein ◽  
Purifying Selection ◽  
Cis Acting ◽  
Genome Wide ◽  
Duplication Events

Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.

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