scholarly journals Functional characterization of mungbean CONSTANS-LIKE genes reveals a key role for CONSTANS-LIKE 2 in the control of flowering time in A. thaliana under short-day conditions

2020 ◽  
Author(s):  
Chenyang Liu ◽  
Qianqian Zhang ◽  
Hong Zhu ◽  
Chunmei Cai ◽  
Shuai Li
Keyword(s):  
Plant Growth ◽  
Flowering Time ◽  
Growth And Development ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Plant Growth And Development ◽  
Promoter Regions ◽  
Short Day ◽  
Long Day ◽  
Close Phylogenetic Relationship

Abstract Background: CONSTANS-LIKE (COL) genes play important roles in the regulation of plant growth and development, and they have been analyzed in many plant species. However, few investigations have examined COL genes in mungbean (Vigna radiata).Results: In this study, we identified and characterized a total 14 of VrCOL genes from mungbean, which distributed on 7 of the 11 mungbean chromosomes. Based on their conserved domains, VrCOLs were clustered into three groups (I, II and III), which contained 4, 5 and 5 members, respectively. The gene structures and conserved motifs of the VrCOL genes were analyzed, and two duplicated gene pairs, VrCOL1/VrCOL2 and VrCOL8/VrCOL9, were identified. A total of 82 cis-acting elements were found in the VrCOL promoter regions, and the numbers and types of cis-acting elements in each VrCOL promoter region differed. As a result, the expression patterns of VrCOLs varied in different tissues, and under long day and short day conations throughout the day. Among these VrCOL genes, VrCOL2 showed a close phylogenetic relationship with Arabidopsis thaliana (A. thaliana) CO and displayed daily oscillations in expression under short day conditions but not long day conditions. In addition, overexpression of VrCOL2 accelerated flowering in A. thaliana under short day conditions by activating the expression of flowering time gene AtFT and AtTSF.Conclusion: Overall, we identified 14 VrCOL genes from mungbean using genome-wide identification. Characteristics and transcription pattern analysis of VrCOL genes revealed their important roles in plant growth and development, and our results suggested that VrCOL2 regulate flowering time under short day conditions in A. thaliana. Our study lays the foundation for further dissection of VrCOL gene functions.

scholarly journals Functional characterization of mungbean CONSTANS-LIKE genes reveals a key role for CONSTANS-LIKE 2 in the control of flowering time under short-day conditions

2020 ◽  
Author(s):  
Chenyang Liu ◽  
Qianqian Zhang ◽  
Hong Zhu ◽  
Chunmei Cai ◽  
Shuai Li
Keyword(s):  
Plant Growth ◽  
Flowering Time ◽  
Growth And Development ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Plant Growth And Development ◽  
Promoter Regions ◽  
Short Day ◽  
Close Phylogenetic Relationship ◽  
Gene Structures

Abstract Background CONSTANS-LIKE (COL) genes play important roles in the regulation of plant growth and development, and they have been analyzed in many plant species. However, few investigations have examined COL genes in mungbean (Vigna radiata). Results In this study, we identified and characterized a total 14 of VrCOL genes from mungbean, which distributed on 7 of the 11 mungbean chromosomes. Based on their conserved domains, VrCOLs were clustered into three groups (I, II and III), which contained 4, 5 and 5 members, respectively. The gene structures and conserved motifs of the VrCOL genes were analyzed, and two duplicated gene pairs, VrCOL2/VrCOL5 and VrCOL6/VrCOL9, were identified. A total of 82 cis-acting elements were found in the VrCOL promoter regions, and the numbers and types of cis-acting elements in each VrCOL promoter region differed. As a result, VrCOLs showed distinct expression patterns in different tissues. Among these VrCOL genes, VrCOL2 showed a close phylogenetic relationship with Arabidopsis thaliana (A. thaliana) CO and displayed daily oscillations in expression under short day conditions but not long day conditions. In addition, overexpression of VrCOL2 accelerated flowering in A. thaliana under short day conditions by activating the expression of flowering time gene FT and TSF. Conclusion Overall, we identified 14 VrCOL genes from mungbean using genome-wide identification. Characteristics and transcription pattern analysis of VrCOL genes revealed their important roles in plant growth and development, and our results suggested that VrCOL2 regulate flowering time under short day conditions. Our study lays the foundation for further dissection of VrCOL gene functions.

scholarly journals Characterization of Mungbean CONSTANS-LIKE Genes and Functional Analysis of CONSTANS-LIKE 2 in the Regulation of Flowering Time in Arabidopsis

2021 ◽  
Vol 12 ◽  
Author(s):  
Chenyang Liu ◽  
Qianqian Zhang ◽  
Hong Zhu ◽  
Chunmei Cai ◽  
Shuai Li
Keyword(s):  
Flowering Time ◽  
Expression Patterns ◽  
Plant Growth And Development ◽  
Promoter Regions ◽  
Short Day ◽  
Long Day ◽  
Close Phylogenetic Relationship ◽  
Gene Functions ◽  
Gene Structures

CONSTANS-LIKE (COL) genes play important roles in the regulation of plant growth and development, and they have been analyzed in many plant species. However, few studies have examined COL genes in mungbean (Vigna radiata). In this study, we identified and characterized 31 mungbean genes whose proteins contained B-Box domains. Fourteen were designated as VrCOL genes and were distributed on 7 of the 11 mungbean chromosomes. Based on their phylogenetic relationships, VrCOLs were clustered into three groups (I, II, and III), which contained 4, 6, and 4 members, respectively. The gene structures and conserved motifs of the VrCOL genes were analyzed, and two duplicated gene pairs, VrCOL1/VrCOL2 and VrCOL8/VrCOL9, were identified. A total of 82 cis-acting elements were found in the VrCOL promoter regions, and the numbers and types of cis-acting elements in each VrCOL promoter region differed. As a result, the expression patterns of VrCOLs varied in different tissues and throughout the day under long-day and short-day conditions. Among these VrCOL genes, VrCOL2 showed a close phylogenetic relationship with Arabidopsis thaliana CO and displayed daily oscillations in expression under short-day conditions but not long-day conditions. In addition, overexpression of VrCOL2 accelerated flowering in Arabidopsis under short-day conditions by affecting the expression of the flowering time genes AtFT and AtTSF. Our study lays the foundation for further investigation of VrCOL gene functions.

scholarly journals Identification of Phytochrome-Interacting Factor Family Members and Functional Analysis of MdPIF4 in Malus domestica

2020 ◽  
Vol 21 (19) ◽  
pp. 7350
Author(s):  
Peng-Fei Zheng ◽  
Xun Wang ◽  
Yu-Ying Yang ◽  
Chun-Xiang You ◽  
Zhen-Lu Zhang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Malus Domestica ◽  
Transcriptional Activation ◽  
Growth And Development ◽  
Abiotic Factors ◽  
Expression Patterns ◽  
Plant Growth And Development ◽  
Promoter Regions ◽  
Helix Loop Helix ◽  
Woody Crop

Phytochrome-interacting factors (PIFs), members of the basic helix-loop-helix transcription factor family that have been extensively investigated in Arabidopsis thaliana, play essential roles in plant growth and development. However, PIF members have not been systematically investigated in apples, a worldwide perennial woody crop of economic importance. Here, seven PIF genes were identified from the Malus × domestica reference genome. Chromosomal locations, gene structures, and phylogenetic relationships of these members were analyzed. Analysis of cis-acting elements in promoter regions of MdPIF genes indicated that various elements were related to light, abiotic stress, and plant hormone responsiveness. Subsequently, subcellular localization and transcriptional activity analysis revealed that MdPIFs were typical nuclear transcription factors with transcriptional activation ability. Expression analysis demonstrated that MdPIF genes had different gene expression patterns for various abiotic factors. Moreover, overexpressed MdPIF4 reduced the sensitivity of apple calluses to abscisic acid (ABA). Our work lays foundations for further investigation of PIF functions in plant growth and development in apples.

scholarly journals Genome-Wide Identification and Comparative Analysis of ARF Family Genes in Three Apiaceae Species

2021 ◽  
Vol 11 ◽  
Author(s):  
Qiaoying Pei ◽  
Nan Li ◽  
Qihang Yang ◽  
Tong Wu ◽  
Shuyan Feng ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Growth And Development ◽  
Expression Patterns ◽  
Gene Families ◽  
Plant Growth And Development ◽  
Response Factors ◽  
Auxin Response Factors ◽  
Functional Analyses ◽  
Significant Positive Selection

The family Apiaceae includes many important vegetables and medicinal plants. Auxin response factors (ARFs) play critical roles in regulating plant growth and development. Here, we performed a comprehensive analysis of the ARF gene family in three Apiaceae species, celery, coriander, and carrot, and compared the results with the ARF gene family of lettuce, Arabidopsis, and grape. We identified 156 ARF genes in all six species and 89 genes in the three Apiaceae species, including 28, 34, and 27 in celery, coriander, and carrot, respectively. The paralogous gene number in coriander was far greater than that in carrot and celery. Our analysis revealed that ARF genes of the three Apiaceae species in 34 branches of the phylogenetic tree underwent significant positive selection. Additionally, our findings indicated that whole-genome duplication played an important role in ARF gene family expansion. Coriander contained a greater number of ARF genes than celery and carrot because of more gene duplications and less gene losses. We also analyzed the expression of ARF genes in three tissues by RNA-seq and verified the results by quantitative real-time PCR. Furthermore, we found that several paralogous genes exhibited divergent expression patterns. Overall, this study provides a valuable resource for exploring how ARF family genes regulate plant growth and development in other plants. Since this is the first report of the ARF gene family in Apiaceae, our results will serve as a guide for comparative and functional analyses of ARF and other gene families in Apiaceae.

scholarly journals Genome-wide identification, genomic organization, and expression profiling of the CONSTANS-like (COL) gene family in petunia under multiple stresses

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Khadiza Khatun ◽  
Sourav Debnath ◽  
Arif Hasan Khan Robin ◽  
Antt Htet Wai ◽  
Ujjal Kumar Nath ◽  
...  
Keyword(s):  
Stress Response ◽  
Plant Growth ◽  
Growth And Development ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Plant Growth And Development ◽  
Specific Expression ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background CONSTANS-like (CO-like, COL) are putative zinc-finger transcription factors known to play vital role in various plant biological processes such as control of flowering time, regulation of plant growth and development and responses to stresses. However, no systematic analysis of COL family gene regarding the plant development and stress response has been previously performed in any solanaceous crop. In the present study, a comprehensive genome-wide analysis of COL family genes in petunia has been conducted to figure out their roles in development of organs and stress response. Results A total of 33 COL genes, 15 PaCOL genes in P. axillaris and 18 PiCOL genes in P. inflata, were identified in petunia. Subsequently, a genome-wide systematic analysis was performed in 15 PaCOL genes. Considering the domain composition and sequence similarity the 15 PaCOL and 18 PiCOL genes were phylogenetically classified into three groups those are conserved among the flowering plants. Moreover, all of the 15 PaCOL proteins were localized in nucleus. Furthermore, differential expression patterns of PaCOL genes were observed at different developmental stages of petunia. Additionally, transcript expression of 15 PaCOL genes under various abiotic and phytohormone treatments showed their response against stresses. Moreover, several cis-elements related to stress, light-responsive, hormone signaling were also detected in different PaCOL genes. Conclusion The phylogenetic clustering, organ specific expression pattern and stress responsive expression profile of conserved petunia COL genes indicating their involvement in plant growth and development and stress response mechanism. This work provide a significant foundation for understanding the biological roles of petunia COL genes in plant growth, development and in stress response.

scholarly journals Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)

2020 ◽  
Author(s):  
Huanhuan Wu ◽  
Lei Zheng ◽  
Ghulam Qanmber ◽  
Mengzhen Guo ◽  
Zhi Wang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Gene Structure ◽  
Growth And Development ◽  
Expression Patterns ◽  
Plant Tolerance ◽  
Plant Growth And Development ◽  
Functional Studies ◽  
Cotton Species ◽  
Plant Homeodomain

Abstract Background: The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information. Plant homeodomain (PHD) protein family has been reported to be involved in regulating various biological processes in plants. However, their functional studies have not yet been carried out in cotton. Results: In this study, 108, 55, and 52 PHD genes were identified in G. hirsutum, G. raimondii, and G. arboreum, respectively. A total of 297 PHD genes from three cotton species, Arabidopsis, and rice were divided into five groups. We performed chromosomal location, phylogenetic relationship, gene structure, and conserved domain analysis for GhPHD genes. GhPHD genes were unevenly distributed on each chromosome, however, more GhPHD genes were distributed on At_05, Dt_05, and At_07 chromosomes. GhPHD proteins depicted conserved domains, and GhPHD genes exhibiting similar gene structure were clustered together. Further, whole genome duplication analysis indicated that purification selection greatly contributed to the functional maintenance of GhPHD gene family. Expression pattern analysis based on RNA-seq data showed that most GhPHD genes showed clear tissue-specific spatiotemporal expression patterns elucidating the multiple functions of GhPHDs in plant growth and development. Moreover, analysis of cis-acting elements revealed that GhPHDs may respond to a variety of abiotic and phytohormonal stresses. In this regard, some GhPHD genes showed good response against abiotic and phytohormonal stresses. Additionally, co-expression network analysis indicated that GhPHDs are essential for plant growth and development, while GhPHD genes response against abiotic and phytohormonal stresses may help to improve plant tolerance in adverse environmental conditions. Conclusion: This study will provide useful information to facilitate further research related to the vital roles of GhPHD gene family in plant growth and development.

scholarly journals Genome-wide analysis of metallothionein gene family in maize to reveal its role in development and stress resistance to heavy metal

2022 ◽  
Vol 55 (1) ◽  
Author(s):  
Canhong Gao ◽  
Kun Gao ◽  
Huixian Yang ◽  
Tangdan Ju ◽  
Jingyi Zhu ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Plant Growth ◽  
Stress Resistance ◽  
Binding Sites ◽  
Growth And Development ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Plant Growth And Development ◽  
Specific Expression

Abstract Background Maize (Zea mays L.) is a widely cultivated cereal and has been used as an optimum heavy metal phytoremediation crop. Metallothionein (MT) proteins are small, cysteine-rich, proteins that play important roles in plant growth and development, and the regulation of stress response to heavy metals. However, the MT genes for maize have not been fully analyzed so far. Methods The putative ZmMT genes were identified by HMMER.The heat map of ZmMT genes spatial expression analysis was generated by using R with the log2 (FPKM + 1).The expression profiles of ZmMT genes under three kinds of heavy metal stresses were quantified by using qRT-PCR. The metallothionein proteins was aligned using MAFFT and phylogenetic analysis were constructed by ClustalX 2.1. The protein theoretical molecular weight and pI, subcellular localization, TFs binding sites, were predicted using ProtParam, PSORT, PlantTFDB, respectively. Results A total of 9 ZmMT genes were identified in the whole genome of maize. The results showed that eight of the nine ZmMT proteins contained one highly conserved metallothio_2 domain, while ZmMT4 contained a Metallothio_PEC domain. All the ZmMT proteins could be classified into three major groups and located on five chromosomes. The ZmMT promoters contain a large number of hormone regulatory elements and hormone-related transcription factor binding sites. The ZmMT genes exhibited spatiotemporal specific expression patterns in 23 tissues of maize development stages and showed the different expression patterns in response to Cu, Cd, and Pb heavy metal stresses. Conclusions We identified the 9 ZmMT genes, and explored their conserved motif, tissue expression patterns, evolutionary relationship. The expression profiles of ZmMT genes under three kinds of heavy metal stresses (Cu, Cd, Pb) were analyzed. In summary, the expression of ZmMTs have poteintial to be regulated by hormones. The specific expression of ZmMTs in different tissues of maize and the response to different heavy metal stresses are revealed that the role of MT in plant growth and development, and stress resistance to heavy metals.

scholarly journals A Novel Insight into Functional Divergence of the MST Gene Family in Rice Based on Comprehensive Expression Patterns

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 239 ◽  
Author(s):  
Xiaolong Deng ◽  
Baoguang An ◽  
Hua Zhong ◽  
Jing Yang ◽  
Weilong Kong ◽  
...  
Keyword(s):  
Plant Growth ◽  
Abiotic Stresses ◽  
Growth And Development ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Rice Genome ◽  
Signal Molecules ◽  
Plant Growth And Development ◽  
Strong Negative Selection ◽  
Insight Into

Sugars are critical for plant growth and development as suppliers of carbon and energy, as signal molecules, or as solute molecules for osmotic homeostasis. Monosaccharide transporter (MST) genes are involved in various processes of plant growth and development as well as in response to abiotic stresses. However, the evolution and their roles of MST genes in growth and development and in coping with abiotic stresses in rice are poorly known. Here, we identified 64 MST genes in rice genome, which are classified into seven subfamilies: STP, PLT, AZT, ERD, pGlcT, INT, and XTPH. MST genes are not evenly distributed between chromosomes (Chrs) with a bias to Chr 3, 4, 7, and 11, which could be a result of duplication of fragments harboring MST genes. In total, 12 duplication events were found in the rice MST family, among which, two pairs were derived from fragmental duplications and ten pairs were from tandem duplications. The synonymous and nonsynonymous substitution rates of duplicate gene pairs demonstrated that the MST family was under a strong negative selection during the evolution process. Furthermore, a comprehensive expression analysis conducted in 11 different tissues, three abiotic stresses, five hormone treatments, and three sugar treatments revealed different expression patterns of MST genes and indicated diversified functions of them. Our results suggest that MST genes play important roles not only in various abiotic stresses but also in hormone and sugar responses. The present results will provide a vital insight into the functional divergence of the MST family in the future study.

scholarly journals Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)

2020 ◽  
Author(s):  
Huanhuan Wu ◽  
Lei Zheng ◽  
Ghulam Qanmber ◽  
Mengzhen Guo ◽  
Zhi Wang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Gene Structure ◽  
Growth And Development ◽  
Expression Patterns ◽  
Plant Tolerance ◽  
Plant Growth And Development ◽  
Functional Studies ◽  
Cotton Species ◽  
Plant Homeodomain

Abstract Background: The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information. Plant homeodomain (PHD) protein family has been reported to be involved in regulating various biological processes in plants. However, their functional studies have not yet been carried out in cotton.Results: In this study, 108, 55, and 52 PHD genes were identified in G. hirsutum, G. raimondii, and G. arboreum, respectively. A total of 297 PHD genes from three cotton species, Arabidopsis, and rice were divided into five groups. We performed chromosomal location, phylogenetic relationship, gene structure, and conserved domain analysis for GhPHD genes. GhPHD genes were unevenly distributed on each chromosome. However, more GhPHD genes were distributed on At_05, Dt_05, and At_07 chromosomes. GhPHD proteins depicted conserved domains, and GhPHD genes exhibiting similar gene structure were clustered together. Further, whole genome duplication (WGD) analysis indicated that purification selection greatly contributed to the functional maintenance of GhPHD gene family. Expression pattern analysis based on RNA-seq data showed that most GhPHD genes showed clear tissue-specific spatiotemporal expression patterns elucidating the multiple functions of GhPHDs in plant growth and development. Moreover, analysis of cis-acting elements revealed that GhPHDs may respond to a variety of abiotic and phytohormonal stresses. In this regard, some GhPHD genes showed good response against abiotic and phytohormonal stresses. Additionally, co-expression network analysis indicated that GhPHDs are essential for plant growth and development, while GhPHD genes response against abiotic and phytohormonal stresses may help to improve plant tolerance in adverse environmental conditions.Conclusion: This study will provide useful information to facilitate further research related to the vital roles of GhPHD gene family in plant growth and development.

scholarly journals Genome-wide identification and transcript analysis of TCP transcription factors in grapevine

2019 ◽  
Author(s):  
xiangpeng leng ◽  
Hongru Wei ◽  
Xiaozhao Xu ◽  
Sandip A. Ghuge ◽  
Dongjie Jia ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Fruit Development ◽  
Growth And Development ◽  
Expression Patterns ◽  
Class Ii ◽  
Plant Growth And Development ◽  
Specific Expression ◽  
Genome Wide ◽  
Tcp Family

Abstract Background The plant-specific TCP transcription factors play different functions in multiple processes of plant growth and development. TCP family genes have been identified in several plant species, but no comprehensive analysis of the TCP family in grapevine has been undertaken to date, especially their roles in fruit development. Results A total of 18 non-redundant grapevine TCP (VvTCP) genes distributing on 11 chromosomes were identified. Phylogenetic and structural analysis showed that VvTCP genes were divided into two main classes - class I and class II. The Class II genes were further classified into two subclasses, the CIN subclass and the CYC/TB1 subclass. Segmental duplication was a predominant duplication event which caused the expansion of VvTCP genes. The cis-acting elements analysis and tissue-specific expression patterns of VvTCP genes demonstrated that these VvTCP genes might play important roles in plant growth and development. Expression patterns of VvTCP genes during fruit development and ripening were analyzed by RNA-Seq and qRT-PCR. Among them, eleven VvTCP genes were down-regulated during different fruit developmental stages, while only one VvTCP genes were up-regulated, suggesting that most VvTCP genes were probably related to early development in grapevine fruit. Futhermore, the expression of most VvTCP genes can be inhibited by drought and waterlogging stresses. Conclusions Our study establishes the first genome-wide analysis of the grapevine TCP gene family and provides valuable information for understanding the classification and functions of the TCP genes in grapevine.

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