scholarly journals Genome-Wide Characterization and Expression Analysis Provide Basis to the Biological Function of Cotton FBA Genes

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhong-Qing Li ◽  
Yao Zhang ◽  
He Li ◽  
Ting-Ting Su ◽  
Cheng-Gong Liu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Function Analysis ◽  
Pcr Analysis ◽  
Functional Domain ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Identification And Characterization

Fructose-1,6-biphosphate aldolase (FBA) is a multifunctional enzyme in plants, which participates in the process of Calvin-Benson cycle, glycolysis and gluconeogenesis. Despite the importance of FBA genes in regulating plant growth, development and abiotic stress responses, little is known about their roles in cotton. In the present study, we performed a genome-wide identification and characterization of FBAs in Gossypium hirsutum. Totally seventeen GhFBA genes were identified. According to the analysis of functional domain, phylogenetic relationship, and gene structure, GhFBA genes were classified into two subgroups. Furthermore, nine GhFBAs were predicted to be in chloroplast and eight were located in cytoplasm. Moreover, the promoter prediction showed a variety of abiotic stresses and phytohormone related cis-acting elements exist in the 2k up-stream region of GhFBA. And the evolutionary characteristics of cotton FBA genes were clearly presented by synteny analysis. Moreover, the results of transcriptome and qRT-PCR analysis showed that the expression of GhFBAs were related to the tissue distribution, and further analysis suggested that GhFBAs could respond to various abiotic stress and phytohormonal treatments. Overall, our systematic analysis of GhFBA genes would not only provide a basis for the understanding of the evolution of GhFBAs, but also found a foundation for the further function analysis of GhFBAs to improve cotton yield and environmental adaptability.

scholarly journals Identification and Characterization of the Glutathione Peroxidase (GPX) Gene Family in Watermelon and Its Expression under Various Abiotic Stresses

Agronomy ◽  
2018 ◽  
Vol 8 (10) ◽  
pp. 206 ◽  
Author(s):  
Yong Zhou ◽  
Jingwen Li ◽  
Junhong Wang ◽  
Wenting Yang ◽  
Youxin Yang
Keyword(s):  
Abiotic Stress ◽  
Glutathione Peroxidase ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Cis Acting ◽  
Genome Wide ◽  
A Genome ◽  
Identification And Characterization ◽  
Lower Expression

Plant glutathione peroxidase (GPX) is an important antioxidant enzyme to maintain H2O2 homeostasis and regulate plant response to abiotic stress. In this paper, we present the first report of a genome-wide identification of GPX genes in watermelon. A total of six genes (ClGPX1–ClGPX6) were identified, which were unevenly located on four chromosomes of the watermelon genome. Based on phylogenetic analysis, the GPX genes of Arabidopsis, rice, cucumber, and sorghum were classified into four groups. Through analyzing the promoter regions of ClGPX genes, many development-, stress-, and hormone-responsive cis-acting regulatory elements were also identified. Expression pattern analysis by qRT-PCR indicated that all ClGPX genes were actively expressed in flowers and fruits, and exhibited relatively lower expression in other tissues, particularly roots and stems. In addition, the expression of ClGPX genes was significantly induced by salt, drought, and cold stresses, as well as abscisic acid (ABA) treatment at different time points, suggesting that they may be involved in response to abiotic stress and ABA. Taken together, our findings demonstrated that ClGPX genes might function in watermelon development, especially in flower and fruit tissue, as well as in response to abiotic stress and hormones.

Genome wide identification and characterization of abiotic stress responsive lncRNAs in Capsicum annuum

2021 ◽  
Author(s):  
Pooja Moni Baruah ◽  
Debasish B. Krishnatreya ◽  
Kuntala Sarma Bordoloi ◽  
Sarvajeet Singh Gill ◽  
Niraj Agarwala
Keyword(s):  
Abiotic Stress ◽  
Capsicum Annuum ◽  
Genome Wide ◽  
Identification And Characterization

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 expression analysis of the VQ gene family in Cicer arietinum and Medicago truncatula

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8471 ◽  
Author(s):  
Lei Ling ◽  
Yue Qu ◽  
Jintao Zhu ◽  
Dan Wang ◽  
Changhong Guo
Keyword(s):  
Cicer Arietinum ◽  
Medicago Truncatula ◽  
Stress Responses ◽  
Pcr Analysis ◽  
Biotic And Abiotic Stress ◽  
Systematic Analysis ◽  
Genome Wide ◽  
Specific Proteins ◽  
Solid Foundation ◽  
In Silico Analyses

Valine-glutamine (VQ) proteins are plant-specific proteins that play crucial roles in plant development as well as biotic and abiotic stress responses. VQ genes have been identified in various plants; however, there are no systematic reports in Cicer arietinum or Medicago truncatula. Herein, we identified 19 and 32 VQ genes in C. arietinum and M. truncatula, respectively. A total of these VQ genes were divided into eight groups (I–VIII) based on phylogenetic analysis. Gene structure analyses and motif patterns revealed that these VQ genes might have originated from a common ancestor. In silico analyses demonstrated that these VQ genes were expressed in different tissues. qRT-PCR analysis indicated that the VQ genes were differentially regulated during multiple abiotic stresses. This report presents the first systematic analysis of VQ genes from C. arietinum and M. truncatula and provides a solid foundation for further research of the specific functions of VQ proteins.

Genome-wide identification of citrus calmodulin-like genes and their expression in response to arbuscular mycorrhizal fungi colonization and drought

2021 ◽  
Author(s):  
Bo Shu ◽  
YaChao Xie ◽  
Fei Zhang ◽  
Dejian Zhang ◽  
Chunyan Liu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Arbuscular Mycorrhizal Fungi ◽  
Stress Responses ◽  
Mycorrhizal Fungi ◽  
Expression Patterns ◽  
Arbuscular Mycorrhizal ◽  
Biotic And Abiotic Stress ◽  
Genome Wide ◽  
A Genome

Calmodulin-like (CML) proteins represent a diverse family of protein in plants, and play significant roles in biotic and abiotic stress responses. However, the involvement of citrus CMLs in plant responses to drought stress (abiotic stress) and arbuscular mycorrhizal fungi (AMF) colonization remain relatively unknown. We characterized the citrus CML genes by analyzing the EF-hand domains and a genome-wide search, and identified a total of 38 such genes, distributed across at least nine chromosomes. Six tandem duplication clusters were observed in the CsCMLs, and 12 CsCMLs exhibited syntenic relationships with Arabidopsis thaliana CMLs. Gene expression analysis showed that 29 CsCMLs were expressed in the roots, and exhibited differential expression patterns. The regulation of CsCMLs expression was not consistent with the cis-elements identified in their promoters. CsCML2, 3, and 5 were upregulated in response to drought stress, and AMF colonization repressed the expression of CsCML7, 9, 12, 13,20, 27, 28, and 35,and induced that of CsCML1, 2, 3, 5, 8, 10, 11, 14, 15, 16, 18, 25, 30, 33, and 37. Furthermore, AMF colonization and drought stress exerted a synergistic effect, evident from the enhanced repression of CsCML7, 9, 12, 13, 27, 28, and 35 and enhanced expression of CsCML2, 3, and 5 under AMF colonization and drought stress. The present study provides valuable insights into the CsCML gene family and its responses to AMF colonization and drought stress.

Genome-wide identification and characterization of UGT family in pigeonpea (Cajanus cajan) and expression analysis in abiotic stress

Trees ◽  
2019 ◽  
Vol 33 (4) ◽  
pp. 987-1002 ◽  
Author(s):  
Zhihua Song ◽  
Lili Niu ◽  
Qing Yang ◽  
Biying Dong ◽  
Litao Wang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Expression Analysis ◽  
Cajanus Cajan ◽  
Genome Wide ◽  
Identification And Characterization

scholarly journals Genome-wide identification and characterization of NBS-encoding genes in Raphanus sativus L. and their roles related to Fusarium oxysporum resistance

2020 ◽  
Author(s):  
Yinbo Ma ◽  
Sushil Satish Chhapekar ◽  
Lu Lu ◽  
Sangheon Oh ◽  
Sonam Singh ◽  
...  
Keyword(s):  
Gene Family ◽  
Fusarium Oxysporum ◽  
Raphanus Sativus ◽  
Expression Profiles ◽  
Recent Common Ancestor ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Encoding Genes ◽  
Identification And Characterization

Abstract Background: The nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are important for plant development and disease resistance. Although genome-wide studies of NBS-encoding genes have been performed in several species, the evolution, structure, expression, and function of these genes remain unknown in radish (Raphanus sativus L.). A recently released draft R. sativus L. reference genome has facilitated the genome-wide identification and characterization of NBS-encoding genes in radish.Results: A total of 225 NBS-encoding genes were identified in the radish genome based on the essential NB-ARC domain through HMM search and Pfam database, with 202 mapped onto nine chromosomes and the remaining 23 localized on different scaffolds. According to a gene structure analysis, we identified 99 NBS-LRR-type genes and 126 partial NBS-encoding genes. Additionally, 80 and 19 genes respectively encoded an N-terminal Toll/interleukin-like domain and a coiled-coil domain. Furthermore, 72% of the 202 NBS-encoding genes were grouped in 48 clusters distributed in 24 crucifer blocks on chromosomes. The U block on chromosomes R02, R04, and R08 had the most NBS-encoding genes (48), followed by the R (24), D (23), E (23), and F (17) blocks. These clusters were mostly homogeneous, containing NBS-encoding genes derived from a recent common ancestor. Tandem (15 events) and segmental (20 events) duplications were revealed in the NBS family. Comparative evolutionary analyses of orthologous genes among Arabidopsis thaliana, Brassica rapa, and Brassica oleracea reflected the importance of the NBS-LRR gene family during evolution. Moreover, examinations of cis-elements identified 70 major elements involved in responses to methyl jasmonate, abscisic acid, auxin, and salicylic acid. According to RNA-seq expression analyses, 75 NBS-encoding genes contributed to the resistance of radish to Fusarium wilt. A quantitative real-time PCR analysis revealed that RsTNL03 (Rs093020) and RsTNL09 (Rs042580) expression positively regulates radish resistance to Fusarium oxysporum, in contrast to the negative regulatory role for RsTNL06 (Rs053740).Conclusions: The NBS-encoding gene structures, tandem and segmental duplications, synteny, and expression profiles in radish were elucidated for the first time and compared with those of other Brassicaceae family members (A. thaliana, B. oleracea, and B. rapa) to clarify the evolution of the NBS gene family. These results may be useful for functionally characterizing NBS-encoding genes in radish.

scholarly journals Genome-Wide Identification, Characterization and Expression Analysis of TCP Transcription Factors in Petunia

2020 ◽  
Vol 21 (18) ◽  
pp. 6594
Author(s):  
Shuting Zhang ◽  
Qin Zhou ◽  
Feng Chen ◽  
Lan Wu ◽  
Baojun Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Leaf Morphogenesis ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome

The plant-specific TCP transcription factors are well-characterized in both monocots and dicots, which have been implicated in multiple aspects of plant biological processes such as leaf morphogenesis and senescence, lateral branching, flower development and hormone crosstalk. However, no systematic analysis of the petunia TCP gene family has been described. In this work, a total of 66 petunia TCP genes (32 PaTCP genes in P. axillaris and 34 PiTCP genes in P. inflata) were identified. Subsequently, a systematic analysis of 32 PaTCP genes was performed. The phylogenetic analysis combined with structural analysis clearly distinguished the 32 PaTCP proteins into two classes—class Ι and class Ⅱ. Class Ⅱ was further divided into two subclades, namely, the CIN-TCP subclade and the CYC/TB1 subclade. Plenty of cis-acting elements responsible for plant growth and development, phytohormone and/or stress responses were identified in the promoter of PaTCPs. Distinct spatial expression patterns were determined among PaTCP genes, suggesting that these genes may have diverse regulatory roles in plant growth development. Furthermore, differential temporal expression patterns were observed between the large- and small-flowered petunia lines for most PaTCP genes, suggesting that these genes are likely to be related to petal development and/or petal size in petunia. The spatiotemporal expression profiles and promoter analysis of PaTCPs indicated that these genes play important roles in petunia diverse developmental processes that may work via multiple hormone pathways. Moreover, three PaTCP-YFP fusion proteins were detected in nuclei through subcellular localization analysis. This is the first comprehensive analysis of the petunia TCP gene family on a genome-wide scale, which provides the basis for further functional characterization of this gene family in petunia.

scholarly journals Genome-Wide Identification and Characterization of AP2/ERF Transcription Factor Family Genes in Oil Palm under Abiotic Stress Conditions

2021 ◽  
Vol 22 (6) ◽  
pp. 2821
Author(s):  
Lixia Zhou ◽  
Rajesh Yarra
Keyword(s):  
Transcription Factor ◽  
Abiotic Stress ◽  
Oil Palm ◽  
Family Members ◽  
Stress Conditions ◽  
Transcription Factor Family ◽  
Genome Wide ◽  
Identification And Characterization ◽  
Erf Transcription Factor

The AP2/ERF transcription factor family members play crucial roles in controlling plant growth and development, as well as responses to various abiotic stresses. Genome-wide identification and characterization of AP2/ERF genes has not yet been carried out in the oil palm genome. In the present work, we reported the occurrence of 172 EgAP2/ERFs (AP2, ERF, RAV & Soloist members) through genome-wide identification. Phylogenetic analysis was used to divide them into four groups, including: 34 AP2, 131 ERF, 5 RAV, and 2 Soloist gene family members. All 172 AP2/ERF members were unevenly distributed across 16 chromosomes of oil palm. Gene duplication analysis elucidated the tandem duplication of AP2/ERFs on chromosome blocks of the oil palm genome during evolution. Gene structure as well as conserved motif analysis demonstrated the conserved nature of intron/exon organization and motifs among the AP2/ERF genes. Several cis-regulatory elements—related to hormone, stress, and defense responses—were identified in the promoter regions of AP2/ERFs. Tissue-specific expression of 172 AP2/ERFs in five different tissues of oil palm was also revealed by heatmap analysis using the available transcriptome data. Finally, abiotic stress (salinity, cold & drought)-responsive AP2/ERFs in the oil palm genome were validated through qPCR analysis. Our study provided valuable information on oil palm AP2/ERF superfamily members and dissected their role in abiotic stress conditions.

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