scholarly journals Genome-Wide Analysis of PEBP Genes in Dendrobium huoshanense: Unveiling the Antagonistic Functions of FT/TFL1 in Flowering Time

2021 ◽  
Vol 12 ◽  
Author(s):  
Cheng Song ◽  
Guohui Li ◽  
Jun Dai ◽  
Hui Deng
Keyword(s):  
Functional Characterization ◽  
Light Response ◽  
Pcr Analysis ◽  
Gene Expressions ◽  
Phylogeny Analysis ◽  
Medicinal Value ◽  
Genome Wide ◽  
Dendrobium Huoshanense ◽  
Flowering Regulation ◽  
Regulatory Functions

Dendrobium is a semi-shade epiphytic Orchidaceae herb with important ornamental and medicinal value. Parts of the cultivation of Dendrobium germplasm resources, as well as the identification of medicinal components, are more studied, but the functional characterization of the flowering regulation in Dendrobium plants is less reported. Here, six PEBP family genes (DhFT3, DhFT1, DhMFT, DhTFL1b, DhFT2, and DhTFL1a) were identified from the Dendrobium huoshanense genome. The chromosome-level mapping showed that these genes were sequentially distributed on chromosomes 6, 9, 15, and 17. The paralogous gene DhTFL1b corresponded to DhTFL1a, which was determined through tandem duplication. The gene structure and conserved motif of DhPEBP indicated five PEBP genes apart from DhMFT contained four exons and three introns entirely. The phylogeny analysis showed that the PEBP gene family in A. thaliana, O. sativa, Z. mays, S. lycopersicum, and P. equestris were classified into three subclades, FT, TFL, and MFT, which maintained a high homology with D. huoshanense. The conserved domain of the amino acid demonstrated that two highly conserved short motifs (DPDXP and GXHR) embed in DhPEBPs, which may contribute to the conformation of the ligand binding bag. The 86th position of DhFTs was tyrosine (Y), while the 83th and 87th of DhTFL1s belonged to histidine (H), suggesting they should have distinct functions in flowering regulation. The promoter of six DhPEBPs contained several cis-elements related to hormone induction, light response, and abiotic stress, which indicated they could be regulated by the environmental stress and endogenous signaling pathways. The qRT-PCR analysis of DhPEBPs in short-term days induced by GA indicated the gene expressions of all DhFTs were gradually increased, whereas the expression of DhTFL1 was decreased. The results implied that DhPEBPs have various regulatory functions in modulating flowering, which will provide a scientific reference for the flowering regulation of Dendrobium plants.

scholarly journals Genome-Wide Analysis of the CCT Gene Family in Chinese White Pear (Pyrus Bretschneideri Rehd.) and Characterization of PbPRR2 in Response to Varying Light Signals

2021 ◽  
Author(s):  
Zheng Liu ◽  
Jia-Li Liu ◽  
Lin An ◽  
Tao Wu ◽  
Li Yang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Light Response ◽  
Purifying Selection ◽  
Photosynthetic Performance ◽  
Negative Regulator ◽  
Canopy Architecture ◽  
Genome Wide

Abstract Background: Canopy architecture is critical in determining the light environment, and subsequently the photosynthetic productivity of fruit crops. Numerous CCT domain-containing genes are crucial for plant adaptive responses to diverse environmental cues. Due to the biological importance of CCT genes, many researchers have focused on their functional characterization. However, little information was available about the CCT genes (PbCCTs) of pear, an important fruit crop.Results: Genome-wide sequence analysis identified 42 putative PbCCTs in the genome of pear (Pyrus bretschneideri Rehd.). Phylogenetic analysis indicated these genes were divided into five subfamilies, namely, COL (14 members), PRR (8 members), ZIM (6 members), TCR1 (6 members) and ASML2 (8 members). Analysis of exon-intron structures and conserved domains provided support for the classification. Genome duplication analysis indicated that segmental duplication events played a crucial role in the expansion of the CCT family in pear, and that the CCT family evolved under the effect of purifying selection. Expression profiles exhibited diverse expression patterns of PbCCTs in various tissues and in response to varying red and blue light. Additionally, transient overexpression of PbPRR2 in Nicotiana benthamiana leaves resulted in inhibition of photosynthetic performance, suggesting that PbPRR2 may be a negative regulator of photosynthesis. Conclusions:This study provides a comprehensive analysis of the CCT gene family in pear and will facilitate further functional investigations of the PbCCTs to uncover their biological roles in light response.

scholarly journals Serotonin and Melatonin Biosynthesis in Plants: Genome-Wide Identification of the Genes and Their Expression Reveal a Conserved Role in Stress and Development

2021 ◽  
Vol 22 (20) ◽  
pp. 11034
Author(s):  
Bidisha Bhowal ◽  
Annapurna Bhattacharjee ◽  
Kavita Goswami ◽  
Neeti Sanan-Mishra ◽  
Sneh L. Singla-Pareek ◽  
...  
Keyword(s):  
Target Genes ◽  
Functional Characterization ◽  
Gene Families ◽  
Pcr Analysis ◽  
Tryptophan Decarboxylase ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Suitable Target

Serotonin (Ser) and melatonin (Mel) serve as master regulators of plant growth and development by influencing diverse cellular processes. The enzymes namely, tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) catalyse the formation of Ser from tryptophan. Subsequently, serotonin N-acetyl transferase (SNAT) and acetyl-serotonin methyltransferase (ASMT) form Mel from Ser. Plant genomes harbour multiple genes for each of these four enzymes, all of which have not been identified. Therefore, to delineate information regarding these four gene families, we carried out a genome-wide analysis of the genes involved in Ser and Mel biosynthesis in Arabidopsis, tomato, rice and sorghum. Phylogenetic analysis unravelled distinct evolutionary relationships among these genes from different plants. Interestingly, no gene family except ASMTs showed monocot- or dicot-specific clustering of respective proteins. Further, we observed tissue-specific, developmental and stress/hormone-mediated variations in the expression of the four gene families. The light/dark cycle also affected their expression in agreement with our quantitative reverse transcriptase-PCR (qRT-PCR) analysis. Importantly, we found that miRNAs (miR6249a and miR-1846e) regulated the expression of Ser and Mel biosynthesis under light and stress by influencing the expression of OsTDC5 and OsASMT18, respectively. Thus, this study may provide opportunities for functional characterization of suitable target genes of the Ser and Mel pathway to decipher their exact roles in plant physiology.

scholarly journals Genome-wide identification and expression analysis of the Collagen family during lactation in water buffalo (Bubalus Bubalis)

2019 ◽  
Author(s):  
Xingrong Lu ◽  
Anqin Duan ◽  
Shasha liang ◽  
Xiaoya Ma ◽  
Chunying Pang ◽  
...  
Keyword(s):  
Mammary Gland ◽  
Structural Integrity ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Basic Structure ◽  
Bubalus Bubalis ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Extracellular Matrix Molecules ◽  
Collagen Genes

Abstract Background: Collagens, as extracellular matrix molecules, support cells for structural integrity and a variety of other functions, thereby contribute to support mammary basic structure and development. However, little information on the identification and expression profiles in response to the mammary gland of the collagen family in buffalo (Bubalus Bubalis) has been reported. Results: A total of 128 buffalo collagen protein sequences corresponding to 45 collagen genes were identified and classified into six clusters based on their phylogenetic relationships, conserved motifs, and gene structure analyses. A transcription factor binding sites (TFBS) analysis inferred that a total of 142 TFBS were predicted within the buffalo collagens, suggesting that different collagen subfamilies harbored different TFBS and played a variety of functions involved in the mammary gland development and lactation. The identified collagen sequences were unequally distributed on 17 chromosomes, 103 of which were determined to be tandem duplicated genes. Transcriptome data and qRT-PCR analysis revealed the expression diversity of buffalo collagen genes in various tissues. Most of the identified collagen genes were significantly up-regulated at the early lactation, 6 collagens upregulated at the peak lactation, and only COL24A1 was up-regulated at the late lactation. Conclusions: The present study provides significant insights into the potential functions of collagen family in dairy buffalo and helps in the functional characterization for collagen genes in further research.

scholarly journals Genome-wide analysis and expression profiles of PdeMYB transcription factors in colored-leaf poplar (Populus deltoids)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Weibing Zhuang ◽  
Xiaochun Shu ◽  
Xinya Lu ◽  
Tao Wang ◽  
Fengjiao Zhang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Green Leaf ◽  
Myb Transcription Factor ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Populus Deltoids

Abstract Background MYB transcription factors, comprising one of the largest transcription factor families in plants, play many roles in secondary metabolism, especially in anthocyanin biosynthesis. However, the functions of the PdeMYB transcription factor in colored-leaf poplar remain elusive. Results In the present study, genome-wide characterization of the PdeMYB genes in colored-leaf poplar (Populus deltoids) was conducted. A total of 302 PdeMYB transcription factors were identified, including 183 R2R3-MYB, five R1R2R3-MYB, one 4R-MYB, and 113 1R-MYB transcription factor genes. Genomic localization and paralogs of PdeMYB genes mapped 289 genes on 19 chromosomes, with collinearity relationships among genes. The conserved domain, gene structure, and evolutionary relationships of the PdeMYB genes were also established and analyzed. The expression levels of PdeMYB genes were obtained from previous data in green leaf poplar (L2025) and colored leaf poplar (QHP) as well as our own qRT-PCR analysis data in green leaf poplar (L2025) and colored leaf poplar (CHP), which provide valuable clues for further functional characterization of PdeMYB genes. Conclusions The above results provide not only comprehensive insights into the structure and functions of PdeMYB genes but also provide candidate genes for the future improvement of leaf colorization in Populus deltoids.

scholarly journals PvB3s: Genome-wide and Transcriptome-wide Identification and Analysis Reveals the B3 Family Regulate Auxin to Resist Salt Stress at the Sprout Stage in Common Bean(P. Vulgaris L. ) .

2020 ◽  
Author(s):  
Qi Zhang ◽  
Wei-jia Li ◽  
Wen-jing Zhang ◽  
Zhen-gong Yin ◽  
Yu-xin Wang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Common Bean ◽  
Dna Sequences ◽  
Functional Characterization ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Genes Expression ◽  
Intron Structure ◽  
Auxin Content

Abstract Background: B3 gene family is a transcription factor family unique to plants, which play an important role in plant growth and development by binding specific DNA sequences. However, data on the B3 genes in the common bean and participate in many abiotic stresses especially salt stress are limited. Result: A total of encoding 100 proteins were identified in common bean. Phylogenetic analysis showed that PvB3s were classified into 4 subgroups, and these clusters were supported by several group-specific features, including exon/intron structure, MEME motifs, and predicted binding site structure. Collinearity analysis showed the connection of PvB3s in the same species and different species. The genes expression pattern showed that PvB3s expressed with a tissue-specific manner during sprout stage. Through RNA-seq and qRT-PCR analysis, it was found that there were differences in expression in extreme materials under salt stress. The determination of auxin content and the analysis of PvB3s expression in the enriched pathway showed that PvB3s would respond to auxin to enhance salt tolerance in common bean sprouting stage. Conclusion: The results provided useful and rich resources of PvB3s for the functional characterization and understanding of B3 transcription factors (TFs) in common bean, which further provides insights that PvB3s may respond to auxin to enhance salt tolerance of common bean.

scholarly journals Genome-wide identification and expression pattern analysis of lipoxygenase gene family in banana

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Fan Liu ◽  
Hua Li ◽  
Junwei Wu ◽  
Bin Wang ◽  
Na Tian ◽  
...  
Keyword(s):  
High Temperature ◽  
Low Temperature ◽  
Pcr Analysis ◽  
Type I ◽  
Segmental Duplications ◽  
Expression Levels ◽  
Genome Wide ◽  
Encoded Proteins ◽  
Gene Structures ◽  
Lipoxygenase Gene Family

AbstractThe LOX genes have been identified and characterized in many plant species, but studies on the banana LOX genes are very limited. In this study, we respectively identified 18 MaLOX, 11 MbLOX, and 12 MiLOX genes from the Musa acuminata, M. balbisiana and M. itinerans genome data, investigated their gene structures and characterized the physicochemical properties of their encoded proteins. Banana LOXs showed a preference for using and ending with G/C and their encoded proteins can be classified into 9-LOX, Type I 13-LOX and Type II 13-LOX subfamilies. The expansion of the MaLOXs might result from the combined actions of genome-wide, tandem, and segmental duplications. However, tandem and segmental duplications contribute to the expansion of MbLOXs. Transcriptome data based gene expression analysis showed that MaLOX1, 4, and 7 were highly expressed in fruit and their expression levels were significantly regulated by ethylene. And 11, 12 and 7 MaLOXs were found to be low temperature-, high temperature-, and Fusarium oxysporum f. sp. Cubense tropical race 4 (FocTR4)-responsive, respectively. MaLOX8, 9 and 13 are responsive to all the three stresses, MaLOX4 and MaLOX12 are high temperature- and FocTR4-responsive; MaLOX6 and MaLOX17 are significantly induced by low temperature and FocTR4; and the expression of MaLOX7 and MaLOX16 are only affected by high temperature. Quantitative real-time PCR (qRT-PCR) analysis revealed that the expression levels of several MaLOXs are regulated by MeJA and FocTR4, indicating that they can increase the resistance of banana by regulating the JA pathway. Additionally, the weighted gene co-expression network analysis (WGCNA) of MaLOXs revealed 3 models respectively for 5 (MaLOX7-11), 3 (MaLOX6, 13, and 17), and 1 (MaLOX12) MaLOX genes. Our findings can provide valuable information for the characterization, evolution, diversity and functionality of MaLOX, MbLOX and MiLOX genes and are helpful for understanding the roles of LOXs in banana growth and development and adaptations to different stresses.

scholarly journals Genome-Wide Analysis and Expression Tendency of Banana (Musa acuminata L.) Calcineurin B-Like (MaCBL) Genes under Potassium Stress

Horticulturae ◽  
2021 ◽  
Vol 7 (4) ◽  
pp. 70
Author(s):  
Ying Xiong ◽  
Ruimei Li ◽  
Xuejun Lin ◽  
Yangjiao Zhou ◽  
Fenlian Tang ◽  
...  
Keyword(s):  
Elongation Factor ◽  
Subcellular Location ◽  
Potassium Deficiency ◽  
Pcr Analysis ◽  
Calcineurin B ◽  
Group I ◽  
Genome Wide ◽  
Ef Hand ◽  
Deficient Medium ◽  
Gene Structures

Calcineurin B-like (CBL) proteins are reported to play significant roles in plant development and ion-transport regulation. Potassium shortages are a serious problem in banana cultivation. However, to date, the members of the banana CBL gene family, and their function in regulating potassium stress, remain unclear. In this study, 11 CBL genes were identified from the banana genome and grouped into four groups (Group I–IV) based on their phylogenetic relationships. The genomic features of these MaCBL genes were analyzed, focusing on their gene structures, standpat motifs, chromosomal distributions, and evolutionary history. Expression pattern analysis revealed that the MaCBLs were function-specific. Further qRT-PCR analysis indicated that the presence of MaCBL2 was indeed a response to potassium deficiency stress. The MaCBL2 gene was cloned, and sequence alignment indicated that it contained four elongation factor hand (EF-hand) domains, the conserved N-terminal myristoylation domain “MGCXXS/K(T)” and the “FPSF” motif. Subcellular location analysis showed that MaCBL2 was located in the plasma membrane, nucleus and cytoplasm. The overexpression of MaCBL2 could restore the growth of the yeast mutant R5421 on a K+-deficient medium. The overexpression of MaCBL2 could promote the root length of transgenic seedlings on K+-deficient medium. These findings indicate that MaCBL2 was, in our study, the key gene of the CBL family in responding to potassium deficiency in bananas. Our discoveries have established a considerable basis for the further study and application of MaCBL genes.

scholarly journals Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 149
Author(s):  
Chao Gong ◽  
Qiangqiang Pang ◽  
Zhiliang Li ◽  
Zhenxing Li ◽  
Riyuan Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gene Families ◽  
High Temperature Stress ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Genome Wide ◽  
Motif Composition ◽  
Hsp Genes ◽  
Identification And Characterization

Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.

scholarly journals Genome-Wide Identification and Analysis of the APETALA2 (AP2) Transcription Factor in Dendrobium officinale

2021 ◽  
Vol 22 (10) ◽  
pp. 5221
Author(s):  
Danqi Zeng ◽  
Jaime A. Teixeira da Silva ◽  
Mingze Zhang ◽  
Zhenming Yu ◽  
Can Si ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Flower Development ◽  
Regulatory Elements ◽  
Negative Control ◽  
Dendrobium Officinale ◽  
Luciferase Reporter ◽  
Pcr Analysis ◽  
Luciferase Reporter Gene ◽  
Genome Wide ◽  
Ap2 Transcription Factor

The APETALA2 (AP2) transcription factors (TFs) play crucial roles in regulating development in plants. However, a comprehensive analysis of the AP2 family members in a valuable Chinese herbal orchid, Dendrobium officinale, or in other orchids, is limited. In this study, the 14 DoAP2 TFs that were identified from the D. officinale genome and named DoAP2-1 to DoAP2-14 were divided into three clades: euAP2, euANT, and basalANT. The promoters of all DoAP2 genes contained cis-regulatory elements related to plant development and also responsive to plant hormones and stress. qRT-PCR analysis showed the abundant expression of DoAP2-2, DoAP2-5, DoAP2-7, DoAP2-8 and DoAP2-12 genes in protocorm-like bodies (PLBs), while DoAP2-3, DoAP2-4, DoAP2-6, DoAP2-9, DoAP2-10 and DoAP2-11 expression was strong in plantlets. In addition, the expression of some DoAP2 genes was down-regulated during flower development. These results suggest that DoAP2 genes may play roles in plant regeneration and flower development in D. officinale. Four DoAP2 genes (DoAP2-1 from euAP2, DoAP2-2 from euANT, and DoAP2-6 and DoAP2-11 from basal ANT) were selected for further analyses. The transcriptional activation of DoAP2-1, DoAP2-2, DoAP2-6 and DoAP2-11 proteins, which were localized in the nucleus of Arabidopsis thaliana mesophyll protoplasts, was further analyzed by a dual-luciferase reporter gene system in Nicotiana benthamiana leaves. Our data showed that pBD-DoAP2-1, pBD-DoAP2-2, pBD-DoAP2-6 and pBD-DoAP2-11 significantly repressed the expression of the LUC reporter compared with the negative control (pBD), suggesting that these DoAP2 proteins may act as transcriptional repressors in the nucleus of plant cells. Our findings on AP2 genes in D. officinale shed light on the function of AP2 genes in this orchid and other plant species.

Sign in / Sign up

Export Citation Format

Share Document