scholarly journals Genome-wide identification and analysis of class III peroxidases in Betula pendula

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Kewei Cai ◽  
Huixin Liu ◽  
Song Chen ◽  
Yi Liu ◽  
Xiyang Zhao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Betula Pendula ◽  
Expression Patterns ◽  
Class Iii ◽  
Physiological Processes ◽  
Plant Life ◽  
Genome Wide ◽  
Plant Life Cycle ◽  
Class Iii Peroxidases ◽  
And Function

Abstract Background Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. At present, POD genes have been studied in Arabidopsis, rice, poplar, maize and Chinese pear, but there are no reports on the identification and function of POD gene family in Betula pendula. Results We identified 90 nonredundant POD genes in Betula pendula. (designated BpPODs). According to phylogenetic relationships, these POD genes were classified into 12 groups. The BpPODs are distributed in different numbers on the 14 chromosomes, and some BpPODs were located sequentially in tandem on chromosomes. In addition, we analyzed the conserved domains of BpPOD proteins and found that they contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results showed that some BpPODs might play an important role in xylem, leaf, root and flower. Furthermore, under low temperature conditions, some BpPODs showed different expression patterns at different times. Conclusions The research on the structure and function of the POD genes in Betula pendula plays a very important role in understanding the growth and development process and the molecular mechanism of stress resistance. These results lay the theoretical foundation for the genetic improvement of Betula pendula.

scholarly journals Genome-Wide Identification and Analysis of Class III Peroxidases in Betula pendula

2020 ◽  
Author(s):  
Kewei Cai ◽  
Song Chen ◽  
Xiyang Zhao ◽  
Su Chen
Keyword(s):  
Stress Responses ◽  
Betula Pendula ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Class Iii ◽  
Physiological Processes ◽  
Genome Wide ◽  
Plant Life Cycle ◽  
Class Iii Peroxidases ◽  
Comprehensive Study

Abstract Background: Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. However, little is known about the POD genes in Betula pendula, although it has been characterized in Arabidopsis, rice and maize. The POD genes remain to be determined in Betula pendula.Results: A total of 90 nonredundant POD genes were identified in Betula pendula. (designated BpPODs). These POD genes were divided into twelve groups based on their phylogenetic relationships. The BpPODs are unevenly distributed on the 14 chromosomes. In addition, some BpPOD genes were located sequentially in tandem on chromosomes, inferred that tandem duplication contributes to the expansion of the POD genes family in Betula pendula. Analysis of the distribution of conserved domains of BpPOD proteins showed that all these proteins contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results show that some BpPOD genes might play significant roles in root, xylem, leaf and flower. Furthermore, under low temperature conditions, some BpPOD genes showed different expression patterns at different times.Conclusions: Comprehensive study of the POD genes suggests that their functional diversity during Betula pendula growth and development. Our findings provide a basis for further functional analysis on POD genes family in Betula pendula.

scholarly journals Genome-Wide Identification and Analysis of Class III Peroxidases in Betula pendula

2020 ◽  
Author(s):  
Kewei Cai ◽  
Song Chen ◽  
Yi Liu ◽  
Xiyang Zhao ◽  
Su Chen
Keyword(s):  
Stress Responses ◽  
Betula Pendula ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Class Iii ◽  
Physiological Processes ◽  
Genome Wide ◽  
Plant Life Cycle ◽  
Class Iii Peroxidases ◽  
Comprehensive Study

Abstract Background: Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. However, little is known about the POD genes in Betula pendula, although it has been characterized in Arabidopsis, rice, poplar, maize and Chinese pear. The POD genes remain to be determined in Betula pendula.Results: A total of 90 nonredundant POD genes were identified in Betula pendula. (designated BpPODs). These POD genes were divided into twelve groups based on their phylogenetic relationships. The BpPODs are unevenly distributed on the 14 chromosomes. In addition, some BpPODs were located sequentially in tandem on chromosomes, inferred that tandem duplication contributes to the expansion of the POD gene family in Betula pendula. Analysis of the distribution of conserved domains of BpPOD proteins showed that all these proteins contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results show that some BpPODs might play significant roles in root, xylem, leaf and flower. Furthermore, under low temperature conditions, some BpPODs showed different expression patterns at different times. Conclusions: Comprehensive study of the POD genes suggests that their functional diversity during Betula pendula growth and development. Our findings provide a basis for further functional analysis on POD gene family in Betula pendula.

scholarly journals Genome-Wide Identification and Analysis of Class III Peroxidases in Betula pendula

2020 ◽  
Author(s):  
Kewei Cai ◽  
Song Chen ◽  
Yi Liu ◽  
Xiyang Zhao ◽  
Su Chen
Keyword(s):  
Stress Responses ◽  
Betula Pendula ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Class Iii ◽  
Physiological Processes ◽  
Genome Wide ◽  
Plant Life Cycle ◽  
Class Iii Peroxidases ◽  
Comprehensive Study

Abstract Background: Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. However, little is known about the POD genes in Betula pendula , although it has been characterized in Arabidopsis , rice and maize. The POD genes remain to be determined in Betula pendula . Results : A total of 90 nonredundant POD genes were identified in Betula pendula . (designated BpPODs ). These POD genes were divided into twelve groups based on their phylogenetic relationships. The BpPODs are unevenly distributed on the 14 chromosomes. In addition, some BpPOD genes were located sequentially in tandem on chromosomes, inferred that tandem duplication contributes to the expansion of the POD genes family in Betula pendula . Analysis of the distribution of conserved domains of BpPOD proteins showed that all these proteins contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results show that some BpPOD genes might play significant roles in root, xylem, leaf and flower. Furthermore, under low temperature conditions, some BpPOD genes showed different expression patterns at different times. Conclusions: Comprehensive study of the POD genes suggests that their functional diversity during Betula pendula growth and development. Our findings provide a basis for further functional analysis on POD genes family in Betula pendula .

scholarly journals Genome-Wide Identification and Analysis of Class III Peroxidases in Betula pendula

2021 ◽  
Author(s):  
Kewei Cai ◽  
Huixin Liu ◽  
Song Chen ◽  
Yi Liu ◽  
Xiyang Zhao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Betula Pendula ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Class Iii ◽  
Physiological Processes ◽  
Genome Wide ◽  
Plant Life Cycle ◽  
Class Iii Peroxidases ◽  
Comprehensive Study

Abstract Background: Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. However, little is known about the POD genes in Betula pendula, although it has been characterized in Arabidopsis, rice, poplar, maize and Chinese pear. The POD genes remain to be determined in Betula pendula.Results: A total of 90 nonredundant POD genes were identified in Betula pendula. (designated BpPODs). These POD genes were divided into twelve groups based on their phylogenetic relationships. The BpPODs are unevenly distributed on the 14 chromosomes. In addition, some BpPODs were located sequentially in tandem on chromosomes, inferred that tandem duplication contributes to the expansion of the POD gene family in Betula pendula. Analysis of the distribution of conserved domains of BpPOD proteins showed that all these proteins contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results show that some BpPODs might play significant roles in root, xylem, leaf and flower. Furthermore, under low temperature conditions, some BpPODs showed different expression patterns at different times. Conclusions: Comprehensive study of the POD genes suggests that their functional diversity during Betula pendula growth and development. Our findings provide a basis for further functional analysis on POD gene family in Betula pendula.

scholarly journals Genome-wide identification and characterization of lectin receptor-like kinase gene family in cucumber and expression profiling analysis under different treatments

2020 ◽  
Author(s):  
Duo Lv ◽  
Gang Wang ◽  
Yue Chen ◽  
Liang-Rong Xiong ◽  
Jing-Xian Sun ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Kinase Gene ◽  
Cucumis Sativus L ◽  
Lectin Receptor ◽  
Genome Wide ◽  
Cucumber Genome ◽  
And Function

Abstract Background Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber ( Cucumis sativus L.).Results In this study, 46 putative LecRLK genes were identified in cucumber genome, including 23 G-type, 22 L-type and 1 C-type LecRLK genes. They unequally distributed on all 7 chromosomes with a clustering trendency. Most of the genes in the cucumber LecRLK (Cs LecRLK) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormone and stress on these genes’ promoters. Transcriptome data demonstrated that distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real time PCR (qRT-PCR) analysis.Conclusion This study provides a better understanding of the evolution and function of LecRLK gene family in cucumber, and opens the possibility to explore the roles that LecRLK s might play in the life cycle of cucumber.

scholarly journals Genome-wide identification and characterization of lectin receptor-like kinase gene family in cucumber and expression profiling analysis under different treatments

2020 ◽  
Author(s):  
Duo Lv ◽  
Gang Wang ◽  
Liang-Rong Xiong ◽  
Jing-Xian Sun ◽  
Yue Chen ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Kinase Gene ◽  
Lectin Receptor ◽  
Genome Wide ◽  
Cucumber Genome ◽  
And Function

Abstract Background: Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber (Cucumis sativus L.). Results: In this study, 46 putative LecRLK genes were identified in cucumber genome, including 23 G-type, 22 L-type and 1 C-type LecRLK genes. They unequally distributed on all 7 chromosomes with a clustering trendency. Most of the genes in the cucumber LecRLK (CsLecRLK) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormone and stress on these genes’ promoters. Transcriptome data demonstrated that distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real time PCR (qRT-PCR) analysis.Conclusion: This study provides a better understanding of the evolution and function of LecRLK gene family in cucumber, and opens the possibility to explore the roles that LecRLKs might play in the life cycle of cucumber.

scholarly journals Genome-Wide Identification and Characterization of Lectin Receptor-Like Kinase Gene Family in Cucumber and Expression Profiling Analysis under Different Treatments

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1032 ◽  
Author(s):  
Duo Lv ◽  
Gang Wang ◽  
Liang-Rong Xiong ◽  
Jing-Xian Sun ◽  
Yue Chen ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Kinase Gene ◽  
Cucumis Sativus L ◽  
Lectin Receptor ◽  
Genome Wide ◽  
And Function

Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber (Cucumis sativus L.). In this study, 46 putative LecRLK genes were identified in the cucumber genome, including 23 G-type and 22 L-type, and one C-type LecRLK gene. They were unequally distributed on all seven chromosomes, with a clustering tendency. Most of the genes in the cucumber LecRLK (CsLecRLK) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormones and stress on these genes’ promoters. Transcriptome data demonstrated distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real-time PCR (qRT-PCR) analysis. This study provides a better understanding of the character and function of the LecRLK gene family in cucumber and opens up the possibility to exploring the roles that LecRLKs might play in the life cycle of cucumber.

scholarly journals Genome-wide identification and characterization of lectin receptor-like kinase gene family in cucumber and expression profiling analysis under different treatments

2020 ◽  
Author(s):  
Duo Lv ◽  
Gang Wang ◽  
Liang-Rong Xiong ◽  
Jing-Xian Sun ◽  
Yue Chen ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Kinase Gene ◽  
Cucumis Sativus L ◽  
Lectin Receptor ◽  
Genome Wide ◽  
And Function

Abstract Background Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber ( Cucumis sativus L.). Results In this study, 46 putative LecRLK genes were identified in cucumber genome, including 23 G-type, 22 L-type and 1 C-type LecRLK genes. They unequally distributed on all 7 chromosomes with a clustering trendency. Most of the genes in the cucumber LecRLK ( Cs ecRLK ) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormone and stress on these genes’ promoters. Transcriptome data demonstrated that distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real time PCR (qRT-PCR) analysis. Conclusion This study provides a better understanding of the evolution and function of LecRLK gene family in cucumber, and opens the possibility to explore the roles that LecRLK s might play in the life cycle of cucumber.

scholarly journals Comprehensive Analysis of the Histone Deacetylase Gene Family in Chinese Cabbage (Brassica rapa): From Evolution and Expression Pattern to Functional Analysis of BraHDA3

Agriculture ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 244
Author(s):  
Seung Hee Eom ◽  
Tae Kyung Hyun
Keyword(s):  
Functional Analysis ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Physiological Processes ◽  
Lysine Residues

Histone deacetylases (HDACs) are known as erasers that remove acetyl groups from lysine residues in histones. Although plant HDACs play essential roles in physiological processes, including various stress responses, our knowledge concerning HDAC gene families and their evolutionary relationship remains limited. In Brassica rapa genome, we identified 20 HDAC genes, which are divided into three major groups: RPD3/HDA1, HD2, and SIR2 families. In addition, seven pairs of segmental duplicated paralogs and one pair of tandem duplicated paralogs were identified in the B. rapa HDAC (BraHDAC) family, indicating that segmental duplication is predominant for the expansion of the BraHDAC genes. The expression patterns of paralogous gene pairs suggest a divergence in the function of BraHDACs under various stress conditions. Furthermore, we suggested that BraHDA3 (homologous of Arabidopsis HDA14) encodes the functional HDAC enzyme, which can be inhibited by Class I/II HDAC inhibitor SAHA. As a first step toward understanding the epigenetic responses to environmental stresses in Chinese cabbage, our results provide a solid foundation for functional analysis of the BraHDAC family.

scholarly journals Genome-wide Identification and Expression Analysis of the YTH Domain-containing RNA-binding Protein Family in Citrus Sinensis

2019 ◽  
Vol 144 (2) ◽  
pp. 79-91 ◽  
Author(s):  
Zhigang Ouyang ◽  
Huihui Duan ◽  
Lanfang Mi ◽  
Wei Hu ◽  
Jianmei Chen ◽  
...  
Keyword(s):  
Stress Responses ◽  
Messenger Rna ◽  
Citrus Sinensis ◽  
Rna Binding ◽  
Developmental Stages ◽  
Rna Binding Proteins ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Genome Wide ◽  
Yth Domain

In eukaryotic systems, messenger RNA regulations, including splicing, 3′-end formation, editing, localization, and translation, are achieved by different RNA-binding proteins and noncoding RNAs. The YTH domain is a newly identified RNA-binding domain that was identified by comparing its sequence with that of splicing factor YT521-B. Previous study showed that the YTH gene plays an important role in plant resistance to abiotic and biotic stress. In this study, 211 YTH genes were identified in 26 species that represent four major plant lineages. Phylogenetic analysis revealed that these genes could be divided into eight subgroups. All of the YTH genes contain a YT521 domain and have different structures. Ten YTH genes were identified in navel orange (Citrus sinensis). The expression profiles of these CitYTH genes were analyzed in different tissues and at different fruit developmental stages, and CitYTH genes displayed distinct expression patterns under heat, cold, salt, and drought stress. Furthermore, expression of the CitYTH genes in response to exogenous hormones was measured. Nuclear localization was also confirmed for five of the proteins encoded by these genes after transient expression in Nicotiana benthamiana cells. This study provides valuable information on the role of CitYTHs in the signaling pathways involved in environmental stress responses in Citrus.

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