Molecular characterization and expression profiles of transcription factor Sox gene family in Culter alburnus

2020 ◽  
Vol 36 ◽  
pp. 119112
Author(s):  
Jianbo Zheng ◽  
Yongyi Jia ◽  
Shili Liu ◽  
Meili Chi ◽  
Shun Cheng ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Gene Family ◽  
Molecular Characterization ◽  
Expression Profiles ◽  
Culter Alburnus ◽  
Sox Gene

scholarly journals Genome-Wide Identification and Transcriptional Expression Profiles of Transcription Factor WRKY in Common Walnut (Juglans regia L.)

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1444
Author(s):  
Fan Hao ◽  
Ge Yang ◽  
Huijuan Zhou ◽  
Jiajun Yao ◽  
Deruilin Liu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Gene Family ◽  
Expression Profiles ◽  
Juglans Regia ◽  
Enrichment Analysis ◽  
Wrky Gene ◽  
Genome Wide ◽  
Plant Pathogen Interaction ◽  
High Degree ◽  
Common Walnut

The transcription factor WRKY is widely distributed in the plant kingdom, playing a significant role in plant growth, development and response to stresses. Walnut is an economically important temperate tree species valued for both its edible nuts and high-quality wood, and its response to various stresses is an important factor that determines the quality of its fruit. However, in walnut trees themselves, information about the WRKY gene family remains scarce. In this paper, we perform a comprehensive study of the WRKY gene family in walnut. In total, we identified 103 WRKY genes in the common walnut that are clustered into 4 groups and distributed on 14 chromosomes. The conserved domains all contained a WRKY domain, and motif 2 was observed in most WRKYs, suggesting a high degree of conservation and similar functions within each subfamily. However, gene structure was significantly differentiated between different subfamilies. Synteny analysis indicates that there were 56 gene pairs in J. regia and A. thaliana, 76 in J. regia and J. mandshurica, 75 in J. regia and J. microcarpa, 76 in J. regia and P. trichocarpa, and 33 in J. regia and Q. robur, indicating that the WRKY gene family may come from a common ancestor. GO and KEGG enrichment analysis showed that the WRKY gene family was involved in resistance traits and the plant-pathogen interaction pathway. In anthracnose-resistant F26 fruits (AR) and anthracnose-susceptible F423 fruits (AS), transcriptome and qPCR analysis results showed that JrWRKY83, JrWRKY73 and JrWRKY74 were expressed significantly more highly in resistant cultivars, indicating that these three genes may be important contributors to stress resistance in walnut trees. Furthermore, we investigate how these three genes potentially target miRNAs and interact with proteins. JrWRKY73 was target by the miR156 family, including 12 miRNAs; this miRNA family targets WRKY genes to enhance plant defense. JrWRKY73 also interacted with the resistance gene AtMPK6, showing that it may play a crucial role in walnut defense.

scholarly journals Global Analysis of WOX Transcription Factor Gene Family in Brassica napus Reveals Their Stress- and Hormone-Responsive Patterns

2018 ◽  
Vol 19 (11) ◽  
pp. 3470 ◽  
Author(s):  
Mang-Mang Wang ◽  
Ming-Ming Liu ◽  
Feng Ran ◽  
Peng-Cheng Guo ◽  
Yun-Zhuo Ke ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Brassica Napus ◽  
Gene Family ◽  
Gene Structure ◽  
Stress Responses ◽  
Expression Profiles ◽  
Global Analysis ◽  
Transcription Factor Gene ◽  
Factor Gene ◽  
Transcription Factor Gene Family

The plant-specific WUSCHEL-related homeobox (WOX) transcription factor gene family is important for plant growth and development but little studied in oil crops. We identified and characterized 58 putative WOX genes in Brassica napus (BnWOXs), which were divided into three major clades and nine subclades based on the gene structure and conserved motifs. Collinearity analysis revealed that most BnWOXs were the products of allopolyploidization and segmental duplication events. Gene structure analysis indicated that introns/exons and protein motifs were conserved in each subclade and RNA sequencing revealed that BnWOXs had narrow expression profiles in major tissues and/or organs across different developmental stages. The expression pattern of each clade was highly conserved and similar to that of the sister and orthologous pairs from Brassica rapa and Brassica oleracea. Quantitative real-time polymerase chain reaction showed that members of the WOX4 subclade were induced in seedling roots by abiotic and hormone stresses, indicating their contribution to root development and abiotic stress responses. 463 proteins were predicted to interact with BnWOXs, including peptides regulating stem cell homeostasis in meristems. This study provides insights into the evolution and expression of the WOX gene family in B. napus and 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

Sign in / Sign up

Export Citation Format

Share Document