scholarly journals Genome-Wide Analysis of the YABBY Transcription Factor Family in Rapeseed (Brassica napus L.)

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 981
Author(s):  
Jichun Xia ◽  
Dong Wang ◽  
Yuzhou Peng ◽  
Wenning Wang ◽  
Qianqian Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Brassica Species ◽  
Pcr Analysis ◽  
Sequencing Data ◽  
Functional Identification ◽  
Brassica Napus L ◽  
Intron Structure ◽  
Duplication Events

The YABBY family of plant-specific transcription factors play important regulatory roles during the development of leaves and floral organs, but their functions in Brassica species are incompletely understood. Here, we identified 79 YABBY genes from Arabidopsis thaliana and five Brassica species (B. rapa, B. nigra, B. oleracea, B. juncea, and B. napus). A phylogenetic analysis of YABBY proteins separated them into five clusters (YAB1–YAB5) with representatives from all five Brassica species, suggesting a high degree of conservation and similar functions within each subfamily. We determined the gene structure, chromosomal location, and expression patterns of the 21 BnaYAB genes identified, revealing extensive duplication events and gene loss following polyploidization. Changes in exon–intron structure during evolution may have driven differentiation in expression patterns and functions, combined with purifying selection, as evidenced by Ka/Ks values below 1. Based on transcriptome sequencing data, we selected nine genes with high expression at the flowering stage. qRT-PCR analysis further indicated that most BnaYAB family members are tissue-specific and exhibit different expression patterns in various tissues and organs of B. napus. This preliminary study of the characteristics of the YABBY gene family in the Brassica napus genome provides theoretical support and reference for the later functional identification of the family genes.

scholarly journals Genome-Wide Characterization and Analysis of Metallothionein Family Genes That Function in Metal Stress Tolerance in Brassica napus L.

2018 ◽  
Vol 19 (8) ◽  
pp. 2181 ◽  
Author(s):  
Yu Pan ◽  
Meichen Zhu ◽  
Shuxian Wang ◽  
Guoqiang Ma ◽  
Xiaohu Huang ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Brassica Napus ◽  
Metal Binding ◽  
Genome Mapping ◽  
Expression Patterns ◽  
Biomass Productivity ◽  
Brassica Species ◽  
Brassica Napus L ◽  
Origin And Evolution ◽  
Duplication Events

Brassica plants exhibit both high biomass productivity and high rates of heavy metal absorption. Metallothionein (MT) proteins are low molecular weight, cysteine-rich, metal-binding proteins that play crucial roles in protecting plants from heavy metal toxicity. However, to date, MT proteins have not been systematically characterized in Brassica. In this study, we identified 60 MTs from Arabidopsis thaliana and five Brassica species. All the MT family genes from Brassica are closely related to Arabidopsis MTs, encoding putative proteins that share similar functions within the same clades. Genome mapping analysis revealed high levels of synteny throughout the genome due to whole genome duplication and segmental duplication events. We analyzed the expression levels of 16 Brassica napus MTs (BnaMTs) by RNA-sequencing and real-time RT-PCR (RT-qPCR) analysis in plants under As3+ stress. These genes exhibited different expression patterns in various tissues. Our results suggest that BnaMT3C plays a key role in the response to As3+ stress in B. napus. This study provides insight into the phylogeny, origin, and evolution of MT family members in Brassica, laying the foundation for further studies of the roles of MT proteins in these important crops.

scholarly journals Genome-Wide Identification and Expression Profiling of Monosaccharide Transporter Genes Associated with High Harvest Index Values in Rapeseed (Brassica napus L.)

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 653
Author(s):  
Liyuan Zhang ◽  
Chao Zhang ◽  
Bo Yang ◽  
Zhongchun Xiao ◽  
Jinqi Ma ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Harvest Index ◽  
Glucose Transporter ◽  
Expression Patterns ◽  
Sugar Transport ◽  
Brassica Species ◽  
Brassica Napus L ◽  
Monosaccharide Transporter ◽  
Sugar Transporters ◽  
Fundamental Information

Sugars are important throughout a plant’s lifecycle. Monosaccharide transporters (MST) are essential sugar transporters that have been identified in many plants, but little is known about the evolution or functions of MST genes in rapeseed (Brassica napus). In this study, we identified 175 MST genes in B. napus, 87 in Brassica oleracea, and 83 in Brassica rapa. These genes were separated into the sugar transport protein (STP), polyol transporter (PLT), vacuolar glucose transporter (VGT), tonoplast monosaccharide transporter (TMT), inositol transporter (INT), plastidic glucose transporter (pGlcT), and ERD6-like subfamilies, respectively. Phylogenetic and syntenic analysis indicated that gene redundancy and gene elimination have commonly occurred in Brassica species during polyploidization. Changes in exon-intron structures during evolution likely resulted in the differences in coding regions, expression patterns, and functions seen among BnMST genes. In total, 31 differentially expressed genes (DEGs) were identified through RNA-seq among materials with high and low harvest index (HI) values, which were divided into two categories based on the qRT-PCR results, expressed more highly in source or sink organs. We finally identified four genes, including BnSTP5, BnSTP13, BnPLT5, and BnERD6-like14, which might be involved in monosaccharide uptake or unloading and further affect the HI of rapeseed. These findings provide fundamental information about MST genes in Brassica and reveal the importance of BnMST genes to high HI in B. napus.

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.

scholarly journals Identification of Flower-Specific Promoters through Comparative Transcriptome Analysis in Brassica napus

2019 ◽  
Vol 20 (23) ◽  
pp. 5949 ◽  
Author(s):  
Yan Li ◽  
Caihua Dong ◽  
Ming Hu ◽  
Zetao Bai ◽  
Chaobo Tong ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Candidate Genes ◽  
Oilseed Rape ◽  
Agronomic Traits ◽  
Expression System ◽  
Expression Patterns ◽  
Gus Expression ◽  
Pcr Analysis ◽  
Transcriptome Data ◽  
Sclerotinia Stem Rot

Brassica napus (oilseed rape) is an economically important oil crop worldwide. Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum is a threat to oilseed rape production. Because the flower petals play pivotal roles in the SSR disease cycle, it is useful to express the resistance-related genes specifically in flowers to hinder further infection with S. sclerotiorum. To screen flower-specific promoters, we first analyzed the transcriptome data from 12 different tissues of the B. napus line ZS11. In total, 249 flower-specific candidate genes with high expression in petals were identified, and the expression patterns of 30 candidate genes were verified by quantitative real-time transcription-PCR (qRT-PCR) analysis. Furthermore, two novel flower-specific promoters (FSP046 and FSP061 promoter) were identified, and the tissue specificity and continuous expression in petals were determined in transgenic Arabidopsis thaliana with fusing the promoters to β-glucuronidase (GUS)-reporter gene. GUS staining, transcript expression pattern, and GUS activity analysis indicated that FSP046 and FSP061 promoter were strictly flower-specific promoters, and FSP046 promoter had a stronger activity. The two promoters were further confirmed to be able to direct GUS expression in B. napus flowers using transient expression system. The transcriptome data and the flower-specific promoters screened in the present study will benefit fundamental research for improving the agronomic traits as well as disease and pest control in a tissue-specific manner.

Molecular Analysis and Expression Patterns of Four 14-3-3 Genes from Brassica napus L.

2010 ◽  
Vol 9 (7) ◽  
pp. 942-950 ◽  
Author(s):  
Gao-miao ZHAN ◽  
Jin TONG ◽  
Han-zhong WANG ◽  
Wei HUA
Keyword(s):  
Brassica Napus ◽  
Molecular Analysis ◽  
Expression Patterns ◽  
Brassica Napus L

scholarly journals Cloning, Sequence Analysis and Expression Patterns during Seed Germination of a Rapeseed (Brassica napus L.) G-x-S-x-G-motif Lipase Gene

2016 ◽  
Vol 44 (2) ◽  
pp. 435-444
Author(s):  
Imen GLAIED GHRAM ◽  
Hatem BELGUITH ◽  
Maha BEN MUSTAPHA ◽  
Issam HIMILA ◽  
Balkiss BOUHAOUALA ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Seed Germination ◽  
Expression Patterns ◽  
Pcr Amplification ◽  
Gene Families ◽  
Lipase Gene ◽  
Homologous Proteins ◽  
Brassica Napus L ◽  
Calculated Molecular Mass ◽  
Hydrolysis Of

Lipases catalyze the hydrolysis of ester bonds in triacylglycerides, generating glycerol and free fatty acids. These enzymes are encoded by extremely complex gene families, and appear to fulfil many different biological functions. Although they are present in all types of organisms, available information on plant lipases is still very limited, as compared to their bacterial and animal counterparts. A full-length clone, BnLIP, encoding a putative lipase, has been isolated by PCR amplification of Brassica napus genomic DNA, with oligonucleotide primers derived from the sequence of an Arabidopsis thaliana homologue. The clone included an open reading frame of 1581 bp encoding a polypeptide of 526 amino acids, with a calculated molecular mass of 59.5 kDa. Analysis of the deduced protein sequence, sequence alignment with homologous proteins from related plant species, and a phylogenetic analysis revealed that the BnLIP protein belongs to the ‘classical’ GxSxG-motif lipase family. RT-PCR assays indicated that the BnLIP gene is expressed specifically, but only transiently, during seed germination: the lipase mRNA was not present at detectable levels in ungerminated seeds, was detected only three days after seed imbibition, but its levels decreased rapidly afterwards. No expression was observed in roots, stems or leaves of adult plants. This expression pattern suggests that BnLIP is one of the lipases involved in the hydrolysis of triacylglycerides stored in rapeseed seeds, ultimately providing nutrients and energy to sustain seedling growth until photosynthesis is activated.

Development of INDELs markers in oilseed rape (Brassica napus L.) using re-sequencing data

2016 ◽  
Vol 36 (6) ◽  
Author(s):  
Sammina Mahmood ◽  
Zhaohong Li ◽  
Xiaopeng Yue ◽  
Bo Wang ◽  
Jun Chen ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Oilseed Rape ◽  
Sequencing Data ◽  
Brassica Napus L

scholarly journals Genome-wide identification and analyses of the AHL gene family in cotton (Gossypium)

2019 ◽  
Author(s):  
Lanjie Zhao ◽  
Youjun Lu ◽  
Wei Chen ◽  
Jinbo Yao ◽  
Yan Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Orthologous Gene ◽  
Potential Functions ◽  
Pcr Analysis ◽  
Type I ◽  
Clade B ◽  
Genome Wide

Abstract Background: Members of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED ( AHL ) family are involved in various plant biological processes via protein-DNA and protein-protein interaction. However, no the systematic identification and analysis of AHL gene family have been reported in cotton. Results: To investigate the potential functions of AHLs in cotton, genome-wide identification, expressions and structure analysis of the AHL gene family were performed in this study. 48, 51 and 99 AHL genes were identified from the G.raimondii, G.arboreum and G.hirsutum genome, respectively. Phylogenetic analysis revealed that the AHLs in cotton evolved into 2 clades, Clade-A with 4-5 introns and Clade-B with intronless (excluding AHL 20-2). Based on the composition of the AT-hook motif(s) and PPC/DUF 296 domain, AHL proteins were classified into three types (Type-I/-II/-III), with Type-I AHLs forming Clade-B, and the other two types together diversifying in Clade-A. The detection of synteny and collinearity showed that the AHLs expanded with the WGD in cotton, and the sequence structure of AHL20-2 showed the tendency of increasing intron in three different Gossypium spp . The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates of orthologous gene pairs revealed that the AHL genes of G.hirsutum had undergone through various selection pressures, purifying selection mainly in A-subgenome and positive selection mainly in D-subgenome. Examination of their expression patterns showed most of AHLs of Clade-B expressed predominantly in stem, while those of Clade-A in ovules, suggesting that the AHLs within each clade shared similar expression patterns with each other. qRT-PCR analysis further confirmed that some GhAHLs higher expression in stems and ovules. Conclusion: In this study, 48, 51 and 99 AHL genes were identified from three cotton genomes respectively. AHLs in cotton were classified into two clades by phylogenetic relationship and three type based on the composition of motif and domain. The AHLs expanded with segmental duplication, not tandem duplication. The expression profiles of GhAHLs revealed abundant differences in expression levels in various tissues and at different stages of ovules development. Our study provided significant insights into the potential functions of AHLs in regulating the growth and development in cotton.

scholarly journals Genome-Wide Characterization of the sHsp Gene Family in Salix suchowensis Reveals Its Functions under Different Abiotic Stresses

2018 ◽  
Vol 19 (10) ◽  
pp. 3246 ◽  
Author(s):  
Jianbo Li ◽  
Jin Zhang ◽  
Huixia Jia ◽  
Zhiqiang Yue ◽  
Mengzhu Lu ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Molecular Characteristics ◽  
Specific Expression ◽  
Cis Acting ◽  
Shsp Gene ◽  
Duplication Events

Small heat shock proteins (sHsps) function mainly as molecular chaperones that play vital roles in response to diverse stresses, especially high temperature. However, little is known about the molecular characteristics and evolutionary history of the sHsp family in Salix suchowensis, an important bioenergy woody plant. In this study, 35 non-redundant sHsp genes were identified in S. suchowensis, and they were divided into four subfamilies (C, CP, PX, and MT) based on their phylogenetic relationships and predicted subcellular localization. Though the gene structure and conserved motif were relatively conserved, the sequences of the Hsp20 domain were diversified. Eight paralogous pairs were identified in the Ssu-sHsp family, in which five pairs were generated by tandem duplication events. Ka/Ks analysis indicated that Ssu-sHsps had undergone purifying selection. The expression profiles analysis showed Ssu-Hsps tissue-specific expression patterns, and they were induced by at least one abiotic stress. The expression correlation between two paralogous pairs (Ssu-sHsp22.2-CV/23.0-CV and 23.8-MT/25.6-MT) were less than 0.6, indicating that they were divergent during the evolution. Various cis-acting elements related to stress responses, hormone or development, were detected in the promoter of Ssu-sHsps. Furthermore, the co-expression network revealed the potential mechanism of Ssu-sHsps under stress tolerance and development. These results provide a foundation for further functional research on the Ssu-sHsp gene family in S. suchowensis.

Sign in / Sign up

Export Citation Format

Share Document