scholarly journals Genome-Wide Identification and Analysis of Class III Peroxidases in Allotetraploid Cotton (Gossypium hirsutum L.) and their Responses to PK Deficiency

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 473 ◽  
Author(s):  
Duan ◽  
Wang ◽  
Chao ◽  
Zhang ◽  
Zhang
Keyword(s):  
Gene Family ◽  
Phylogenetic Relationships ◽  
Upland Cotton ◽  
Tandem Duplication ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Class Iii ◽  
P Deficiency ◽  
Duplication Events ◽  
Class Iii Peroxidases

Class III peroxidases (PODs), commonly known as secretable class III plant peroxidases, are plant-specific enzymes that play critical roles in not only plant growth and development but also the responses to biotic and abiotic stress. In this study, we identified 198 nonredundant POD genes, designated GhPODs, with 180 PODs being predicted to secrete into apoplast. These POD genes were divided into 10 sub-groups based on their phylogenetic relationships. We performed systematic bioinformatic analysis of the POD genes, including analysis of gene structures, phylogenetic relationships, and gene expression profiles. The GhPODs are unevenly distributed on both upland cotton sub-genome A and D chromosomes. Additionally, these genes have undergone 15 segmental and 12 tandem duplication events, indicating that both segmental and tandem duplication contributed to the expansion of the POD gene family in upland cotton. Ka/Ks analysis suggested that most duplicated GhPODs experienced negative selection, with limited functional divergence during the duplication events. High-throughput RNA-seq data indicated that most highly expressed genes might play significant roles in root, stem, leaf, and fiber development. Under K or P deficiency conditions, PODs showed different expression patterns in cotton root and leaf. This study provides useful information for further functional analysis of the POD gene family in upland cotton.

scholarly journals Analysis of PRX Gene Family and Its Function on Cell Lignification in Pears (Pyrus bretschneideri)

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1874
Author(s):  
Zhihua Xie ◽  
Weikang Rui ◽  
Yazhou Yuan ◽  
Xiaofei Song ◽  
Xing Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Phylogenetic Relationships ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Fruit Growth ◽  
Event Analysis ◽  
Class Iii ◽  
Biotic And Abiotic Stress ◽  
Pear Fruit ◽  
Highly Expressed Genes

Class III peroxidases (PRXs) are plant-specific enzymes that play key roles in the responses to biotic and abiotic stress during plant growth and development. In addition, some peroxidases also play roles in plant lignification. In this study, a total of 114 PRX (designated PbPRXs) genes were identified in the pear (Pyrus bretschneideri Rehd) genome based on systematic analysis. These PRX genes were divided into 12 groups based on their phylogenetic relationships. We performed systematic bioinformatics analysis of the PRX genes, including analysis of gene structures, conserved motifs, phylogenetic relationships, and gene expression patterns during pear fruit growth. The PbPRXs are unevenly distributed on the 17 pear chromosomes and some of them on other scaffolds. Gene duplication event analysis indicated that whole-genome duplication (WGD) and segmental duplication play key roles in PRX gene amplification. Ka/Ks analysis suggested that most duplicated PbPRXs experienced purifying selection, with limited functional divergence during the duplication events. Furthermore, the analysis indicated that those highly expressed genes might play significant roles in the lignification of cells to form stone cells in pear fruit. We examined the expression of those highly expressed genes during fruit growth using quantitative real-time PCR (qRT-PCR), verifying differential expression patterns at different stages of fruit. This study provides useful information for further functional analysis of the PRX gene family in pears.

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 expression analysis of the JAZ gene family in turnip

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kai Jia ◽  
Cunyao Yan ◽  
Jing Zhang ◽  
Yunxia Cheng ◽  
Wenwen Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Tandem Duplication ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Specific Protein ◽  
Gene Pairs ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structure And Expression

AbstractJAZ is a plant-specific protein family involved in the regulation of plant development, abiotic stresses, and responses to phytohormone treatments. In this study, we carried out a bioinformatics analysis of JAZ genes in turnip by determining the phylogenetic relationship, chromosomal location, gene structure and expression profiles analysis under stresses. The 36 JAZ genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The JAZ genes were located on 10 chromosomes. Two gene pairs were involved in tandem duplication events. We identified 44 collinear JAZ gene pairs in the turnip genome. Analysis of the Ka/Ks ratios indicated that the paralogs of the BrrJAZ family principally underwent purifying selection. Expression analysis suggested JAZ genes may be involved in the formation of turnip tuberous root, and they also participated in the response to ABA, SA, MeJA, salt stress and low-temperature stress. The results of this study provided valuable information for further exploration of the JAZ gene family in turnip.

Magnetic Bead Adsorption Extraction of Xyloglucan Endoglucosidase/Hydrolase Gene and Its Expression Analysis in Land Cotton

2021 ◽  
Vol 15 (4) ◽  
pp. 478-490
Author(s):  
Xianliang Li ◽  
Hang Liu ◽  
Zhichang Zhao
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Magnetic Bead ◽  
Evolutionary Significance ◽  
Cotton Fibers ◽  
Expression Levels ◽  
Duplication Events ◽  
And Function

The xyloglucan Endotransglucosylase/hydrolase (XTH) genes are proposed to encode enzymes responsible for cleaving and reattaching xyloglucan polymers. Despite prior identification of the XTH gene family in Arabidopsis and rice, the XTH family in upland cotton, a tetraploid plant whose fiber cell is an excellent model for the study of plant cell elongation, is yet uncharacterized. In this study, iron tetroxide based magnetic nanobead (Fe3O4 NPs) was successfully prepared and applied to extract xyloglucan endoglucosidase/hydrolase genes. Analysis of the genes can provide insight into the evolutionary significance and function of the XTH gene family. A total of 41 XTH genes found by searching the phytozomev 10 database were classified into three groups based on their phylogeny and the motifs of individual genes. The 25 and 5 GhXTH genes occurred as clusters resulting from the segmental and tandem duplication. More frequent duplication events in cotton contributed to the expansion of the family. Global microarray analysis of GhXTH gene expression in cotton fibers showed that 18 GhXTH genes could be divided into two clusters and four subclusters based on their expression patterns. Accumulated expression levels were relatively high at the elongation stages of the cotton fibers, suggesting that cotton fiber elongation requires high amounts of the GhXTH protein. The expression profiles of GhXTH3 and GhXTH4 showed by quantitative realtime PCR were similar to those determined by microarray. Additionally, the expression levels of GhXTH3 and GhXTH4 in Gossypium barbadense were higher than those in Gossypium hirsutum at developmental stages, indicating that expression levels of GhXTH3 and GhXTH4 in fibers varied among cultivars differing in fiber length.

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.

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 Analysis and Characterization of the Aux/IAA Family Genes Related to Floral Scent Formation in Hedychium coronarium

2019 ◽  
Vol 20 (13) ◽  
pp. 3235 ◽  
Author(s):  
Yanguo Ke ◽  
Farhat Abbas ◽  
Yiwei Zhou ◽  
Rangcai Yu ◽  
Yuechong Yue ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Floral Scent ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Cut Flowers ◽  
Flower Opening ◽  
Hedychium Coronarium

Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.

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.

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