scholarly journals Expression of Photosynthesis Pathway Gene From Rice and Maize for Understanding Role in Plant Stress and Development Using Bioinformatics Approaches

2020 ◽  
Author(s):  
saurabh pandey ◽  
Vaibhav Raina
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
In Silico ◽  
Chromosome 1 ◽  
Photosynthetic Pathway ◽  
Related Gene ◽  
Motif Analysis ◽  
Pathway Gene ◽  
C4 Pathway ◽  
Signature Motif

Abstract Background Rice and maize go to family Poaceae contains many crops of agronomic trait and also represent two carbon metabolism systems, C3 and C4. Analysis of the maize sequence provides new insights into the employment of C3 genes to the C4 mechanism which allowed us to identify more orthologs in other crops. This investigation reports comparative account of genome wide in silico identification of C4 pathway related genes from Zea maize (Zm) and Oryza sativa (Os) from the available whole genome sequence information. The annotation of gene sequences, signature motif analysis, protein phophorylation analysis, study of upstream cis-acting elements, phylogenetic tree construction, chromosomal locations, syntenic mapping and microarray expression analysis of C4 pathway related gene family from both the genomes have been attempted. Results A total of 30 and 37 C4-pathway genes have been predicted from rice and maize genome respectively. Multiple-sequence-alignment and signature motif analysis of these proteins of rice and maize revealed high conserveness. Phophorylation analysis revealed that maize have high number than rice. The phylogenetic analysis of C4 related genes across both plant species clearly resulted in four sub-groups in both plants. In Rice, the 30 genes of C4 pathway related genes family are distributed on eleven out of twelve chromosomes, while in maize, they are randomly distributed on all the chromosomes. Most of the genes of Zm’s chromosome 1 show syntenic relationship with chromosome 1. The cis-regulatory-elements of Zm and Os genes suggested its diverse functions associated with plant growth development, stress and hormone responsiveness as well as endosperm and meristem specific gene expression. This investigation of Zm and Os can now offer new insights into the role of different C4 pathway related genes and examine the comparative syntenic mapping between two monocot models and allows for better understanding about how genes evolve within monocots. Therefore, in silico investigation of C4-photosynthetic-pathway gene family needs to be supported by wet lab experimentation of the novel genes for elucidating their function in many biological courses.Conclusion Results revealed that photosynthetic pathway related gene play a potent role in stress response and plant growth and development.

scholarly journals Genome wide analysis of kinesin gene family in Citrullus lanatus reveals an essential role in early fruit development

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shujuan Tian ◽  
Jiao Jiang ◽  
Guo-qi Xu ◽  
Tan Wang ◽  
Qiyan Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Hormones ◽  
Fruit Development ◽  
Developmental Stages ◽  
Profile Analysis ◽  
Citrullus Lanatus ◽  
Binding Motif ◽  
Distribution Analysis ◽  
Motif Analysis ◽  
Expression Profile Analysis

Abstract Background Kinesin (KIN) as a motor protein is a versatile nano-machine and involved in diverse essential processes in plant growth and development. However, the kinesin gene family has not been identified in watermelon, a valued and nutritious fruit, and yet their functions have not been characterized. Especially, their involvement in early fruit development, which directly determines the size, shape, yield and quality of the watermelon fruit, remains unclear. Results In this study, we performed a whole-genome investigation and comprehensive analysis of kinesin genes in C. lanatus. In total, 48 kinesins were identified and categorized into 10 kinesin subfamilies groups based on phylogenetic analysis. Their uneven distribution on 11 chromosomes was revealed by distribution analysis. Conserved motif analysis showed that the ATP-binding motif of kinesins was conserved within all subfamilies, but not the microtubule-binding motif. 10 segmental duplication pairs genes were detected by the syntenic and phylogenetic approaches, which showed the expansion of the kinesin gene family in C. lanatus genome during evolution. Moreover, 5 ClKINs genes are specifically and abundantly expressed in early fruit developmental stages according to comprehensive expression profile analysis, implying their critical regulatory roles during early fruit development. Our data also demonstrated that the majority of kinesin genes were responsive to plant hormones, revealing their potential involvement in the signaling pathways of plant hormones. Conclusions Kinesin gene family in watermelon was comprehensively analyzed in this study, which establishes a foundation for further functional investigation of C. lanatus kinesin genes and provides novel insights into their biological functions. In addition, these results also provide useful information for understanding the relationship between plant hormone and kinesin genes in C. lanatus.

scholarly journals Isolation and Characterization Of Rice R Genes: Evidence for Distinct Evolutionary Paths in Rice and Maize

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 1021-1031 ◽  
Author(s):  
Jianping Hu ◽  
Beth Anderson ◽  
Susan R Wessler
Keyword(s):  
Gene Family ◽  
Gene Families ◽  
Chromosome 1 ◽  
R Gene ◽  
R Genes ◽  
Helix Loop Helix ◽  
Isolation And Characterization ◽  
Undetermined Function ◽  
Evolutionary Paths

Abstract R and B genes and their homologues encode basic helix-loop-helix (bHLH) transcriptional activators that regulate the anthocyanin biosynthetic pathway in flowering plants. In maize, R/B genes comprise a very small gene family whose organization reflects the unique evolutionary history and genome architecture of maize. To know whether the organization of the R gene family could provide information about the origins of the distantly related grass rice, we characterized members of the R gene family from rice Oryza sativa. Despite being a true diploid, O. sativa has at least two R genes. An active homologue (Ra) with extensive homology with other R genes is located at a position on chromosome 4 previously shown to be in synteny with regions of maize chromosomes 2 and 10 that contain the B and R loci, respectively. A second rice R gene (Rb) of undetermined function was identified on chromosome 1 and found to be present only in rice species with AA genomes. All non-AA species have but one R gene that is Ra-like. These data suggest that the common ancestor shared by maize and rice had a single R gene and that the small R gene families of grasses have arisen recently and independently.

The SCG10-related gene family in the developing rat retina: Persistent expression of SCLIP and stathmin in mature ganglion cell layer

2000 ◽  
Vol 861 (2) ◽  
pp. 399-407 ◽  
Author(s):  
Toru Nakazawa ◽  
Itsuko Nakano ◽  
Tatsuo Furuyama ◽  
Hiroshi Morii ◽  
Makoto Tamai ◽  
...  
Keyword(s):  
Gene Family ◽  
Ganglion Cell ◽  
Ganglion Cell Layer ◽  
Cell Layer ◽  
Related Gene ◽  
Rat Retina ◽  
Developing Rat

scholarly journals Gene Expression of CCAAT/Enhancer-Binding Protein .DELTA. Mediated by Autoregulation Is Repressed by Related Gene Family Proteins.

2000 ◽  
Vol 23 (12) ◽  
pp. 1424-1429 ◽  
Author(s):  
Atsuhiro TANABE ◽  
Chizumi KUMAHARA ◽  
Shigehiro OSADA ◽  
Tsutomu NISHIHARA ◽  
Masayoshi IMAGAWA
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Binding Protein ◽  
Related Gene ◽  
Enhancer Binding Protein ◽  
Ccaat Enhancer Binding Protein

scholarly journals Silicon flow from root to shoot in pepper: a comprehensive in silico analysis reveals a potential linkage between gene expression and hormone signaling that stimulates plant growth and metabolism

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10053
Author(s):  
Fernando Carlos Gómez-Merino ◽  
Libia Iris Trejo-Téllez ◽  
Atonaltzin García-Jiménez ◽  
Hugo Fernando Escobar-Sepúlveda ◽  
Sara Monzerrat Ramírez-Olvera
Keyword(s):  
Plant Growth ◽  
Plant Species ◽  
In Silico ◽  
In Silico Analysis ◽  
Regulatory Elements ◽  
Plant Tissues ◽  
Promoter Regions ◽  
Root Cells ◽  
Physiological Processes ◽  
Silico Analysis

Background Silicon (Si) is categorized as a quasi-essential element for plants thanks to the benefits on growth, development and metabolism in a hormetic manner. Si uptake is cooperatively mediated by Lsi1 and Lsi2. Nevertheless, Lsi channels have not yet been identified and characterized in pepper (Capsicum annuum), while genes involved in major physiological processes in pepper are Si-regulated. Furthermore, Si and phytohormones may act together in regulating plant growth, metabolism and tolerance against stress. Our aim was to identify potential synergies between Si and phytohormones stimulating growth and metabolism in pepper, based on in silico data. Methods We established a hydroponic system to test the effect of Si (0, 60, 125 and 250 mg L−1 Si) on the concentrations of this element in different pepper plant tissues. We also performed an in silico analysis of putative Lsi genes from pepper and other species, including tomato (Solanum lycopersicum), potato (Solanum tuberosum) and Arabidopsis thaliana, to look for cis-acting elements responsive to phytohormones in their promoter regions. With the Lsi1 and Lsi2 protein sequences from various plant species, we performed a phylogenetic analysis. Taking into consideration the Lsi genes retrieved from tomato, potato and Arabidopsis, an expression profiling analysis in different plant tissues was carried out. Expression of Si-regulated genes was also analyzed in response to phytohormones and different plant tissues and developmental stages in Arabidopsis. Results Si concentrations in plant tissues exhibited the following gradient: roots > stems > leaves. We were able to identify 16 Lsi1 and three Lsi2 genes in silico in the pepper genome, while putative Lsi homologs were also found in other plant species. They were mainly expressed in root tissues in the genomes analyzed. Both Lsi and Si-regulated genes displayed cis-acting elements responsive to diverse phytohormones. In Arabidopsis, Si-regulated genes were transcriptionally active in most tissues analyzed, though at different expressed levels. From the set of Si-responsive genes, the NOCS2 gene was highly expressed in germinated seeds, whereas RABH1B, and RBCS-1A, were moderately expressed in developed flowers. All genes analyzed showed responsiveness to phytohormones and phytohormone precursors. Conclusion Pepper root cells are capable of absorbing Si, but small amounts of this element are transported to the upper parts of the plant. We could identify putative Si influx (Lsi1) and efflux (Lsi2) channels that potentially participate in the absorption and transport of Si, since they are mainly expressed in roots. Both Lsi and Si-regulated genes exhibit cis-regulatory elements in their promoter regions, which are involved in phytohormone responses, pointing to a potential connection among Si, phytohormones, plant growth, and other vital physiological processes triggered by Si in pepper.

scholarly journals Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max)

2019 ◽  
Author(s):  
Yongbin Wang ◽  
Zhenfeng Jiang ◽  
Zhenxiang Li ◽  
Yuanling Zhao ◽  
Weiwei Tan ◽  
...  
Keyword(s):  
Glycine Max ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Biological Functions ◽  
Conserved Domain ◽  
Genome Wide ◽  
Development Processes

Background. VQ proteins, the plant-specific transcription factors, are involved in the regulation of plant growth, development, and stress responses; however, few articles systematic reported VQ genes in the soybean. Methods. In total, we identified 75 GmVQ genes, which were classified into 7 groups (Ⅰ-Ⅶ). Conserved domain analysis indicated that VQ gene family members all contained the VQ domains. The VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed cis-elements related to stress responses, phytohormone responses and controlling physical and reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were expressed in nine tissues suggested their putative function in many aspects of plant growth and development, and response to stresses in Glycine max. Results. The present study provided basic information for further analysis of the biological functions of GmVQ proteins in various development processes.

scholarly journals Genome-Wide Identification of GDSL-Type Esterase/Lipase Gene Family in Dasypyrum villosum L. Reveals That DvGELP53 Is Related to BSMV Infection

2021 ◽  
Vol 22 (22) ◽  
pp. 12317
Author(s):  
Heng Zhang ◽  
Xu Zhang ◽  
Jia Zhao ◽  
Li Sun ◽  
Haiyan Wang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Dasypyrum Villosum ◽  
Promoter Regions ◽  
Lipase Gene ◽  
Long Distance ◽  
Enzyme Superfamily ◽  
Genome Wide ◽  
A Genome ◽  
Long Distance Movement

GDSL-type esterase/lipase proteins (GELPs) characterized by a conserved GDSL motif at their N-terminus belong to the lipid hydrolysis enzyme superfamily. In plants, GELPs play an important role in plant growth, development and stress response. The studies of the identification and characterization of the GELP gene family in Triticeae have not been reported. In this study, 193 DvGELPs were identified in Dasypyrum villosum and classified into 11 groups (clade A–K) by means of phylogenetic analysis. Most DvGELPs contain only one GDSL domain, only four DvGELPs contain other domains besides the GDSL domain. Gene structure analysis indicated 35.2% DvGELP genes have four introns and five exons. In the promoter regions of the identified DvGELPs, we detected 4502 putative cis-elements, which were associated with plant hormones, plant growth, environmental stress and light responsiveness. Expression profiling revealed 36, 44 and 17 DvGELPs were highly expressed in the spike, the root and the grain, respectively. Further investigation of a root-specific expressing GELP, DvGELP53, indicated it was induced by a variety of biotic and abiotic stresses. The knockdown of DvGELP53 inhibited long-distance movement of BSMV in the tissue of D. villosum. This research provides a genome-wide glimpse of the D. villosum GELP genes and hints at the participation of DvGELP53 in the interaction between virus and plants.

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