Genome-wide comprehensive characterization and expression analysis of TLP gene family revealed its responses to hormonal and abiotic stresses in watermelon (Citrullus lanatus)

Ram, Chet; Danish, Shagufta; Kesawat, Mahipal Singh; Panwar, Bhupendra Singh; Verma, Manjusha; Arya, Lalit; Yadav, Sheel; Sharma, Vedprakash

doi:10.1016/j.gene.2022.146818

Cited by 12 publications

(8 citation statements)

References 101 publications

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“…The functional genomic tools and availability of both EST and transcriptome data provided the fundamental basis of gene expression in spatio-temporal and during environmental stress conditions in crop plants. Owing to these advantages, it become easy to decipher digital expression of genes by mapping of EST and short read sequences of transcriptome studies conducted in crop plants (Ram et al 2022). The digital expression analysis of RBOH transcripts have been reported in many crop suggesting the biological activities of RBOH genes against abiotic stress conditions (Begum et al 2024; Sharma et al 2024).…”

Section: Discussionmentioning

confidence: 99%

Genome wide comprehensive characterization and expression analysis of RBOH genes revealed drought stress response in mung bean (Vigna radiate L.)

Dogra,

Ram,

Kesawat

et al. 2024

Preprint

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Respiratory burst oxidase homologs (RBOHs) play a pivotal role as key producer of reactive oxygen species (ROS) during broad range of biological processes including plant growth, development, hormonal signalling and environmental stress responses in plants. Since, the availability of mung bean (Vigna radiata) genome sequences, the identification and characterization of the RBOH gene family in mung bean remain unknown. Therefore, the current study focuses on identifying and characterizing nine RBOH genes, designated as VraRBOH, in mung bean. The VraRBOH genes were characterized using all sort of bioinformatics analysis for distribution, structural and phylogenic organization in mung bean genome. Further, their expression level was assessed during drought stress in mung bean. The chromosomal distribution analysis showed the presence of VraRBOH genes on six chromosomes only rather than scattering in whole genome. All VraRBOH genes exhibited conserved domain including those for binding of FAD, NADPH ribose and NADPH region in C-terminal region during multiple sequence alignment analysis. The VraRBOH genes harboured the introns ranged from 0 (VraRBOH1) to 23 (VraRBOH4). The phylogenetic tree consisted of five major groups with subgroups. The presence of the cis-regulatory elements in the VraRBOH gene promoter regions suggested the biologically active nature of these genes in mung bean. Semi quantitative reverse transcriptase PCR analysis revealed that VraRBOH4 exhibited exponential expression at the transcript level in the time-course experiment of drought stress in mung bean. Conversely, the remaining VraRBOH genes displayed either up- or down-regulation at specific time points of the drought stress treatment. The identified and characterized VraRBOH gene family offers a valuable resource for both fundamental and applied research aimed at comprehending mung bean's tolerance to abiotic stress.

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Section: Discussionmentioning

confidence: 99%

Genome wide comprehensive characterization and expression analysis of RBOH genes revealed drought stress response in mung bean (Vigna radiate L.)

Dogra,

Ram,

Kesawat

et al. 2024

Preprint

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“…Gene duplication is the main mode of gene family expansion, where whole-genome duplications was considered to be an important driver of expansion and an important source of functional diversi cation, and low tandem and high segmental duplications of the TLP gene family were widely observed in plants (Cao, Lv, et al, 2015, Ram, Danish, et al, 2022. Gene duplication analysis showed that thirteen gene duplication events in the whole-genome of watermelon, which included one tandem and twelve segmental duplications (Ram, Danish, et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

“…We also downloaded AtTLPs and OsTLPs protein sequences from Ensembl Plants (http://plants.ensembl.org) and used as query sequence in BLASTp search against P. notoginseng protein sets (Zhang, Chen, et al, 2021, Zhao andSu, 2010). The e-value of 10 − 5 and > 100-bit scores were kept cut off to identify putative TLP genes, and eventually, the BLASTp output was tabulated (Ram, Danish, et al, 2022). We compared the results of the two methods to con rm TLP candidate genes in these species.…”

Section: Identi Cation Of Pntlp Genes and Analysis Of Its Characteris...mentioning

confidence: 99%

Genome-wide identification of thaumatin-like protein family genes in Panax notoginseng and analysis of their responses to Fusarium solani infection

Yang,

Guan,

Wei

et al. 2023

Genet Resour Crop Evol

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Panax notoginseng is the most widely used Chinese medicinal herb, and one main challenge to the successful cultivation is root rot, which signi cantly reduces its yield and quality. Thaumatin-like proteins (TLPs) are a large and complex proteins of pathogenesis-related family 5 (PR-5), which play a important role in plant host defense and other physiological processes. The objective of this study is to identify the TLP gene family in P. notoginseng on a genome-wide scale and explore their response to Fusarium solani infection. In this study, a total of twenty PnTLP genes were identi ed in P. notoginseng genome and divided into ten subfamilies (Group I-X) by the phylogenetic analysis. Subcellular localization prediction showed that most of the PnTLP proteins were located in the extracellular, and few were distributed in chloroplast. Meanwhile, the gene structure and protein conserved domain were established by MEME Suite. Duplication analysis showed that segmental duplication, rather than tandem duplications promoting the expansion of the PnTLPs gene family. The analysis of collinear relationships re ected that there were 36 homologous genes between P. notoginseng and Arabidopsis and 9 between P. notoginseng and rice. Moreover, cis-acting elements of PnTLP gene promoters were predicted which indicated that PnTLPs are involved in biotic, abiotic stress, and hormone induction. Expression pro le analysis revealed the possible roles of TLPs in plant development and fungal stress response. Furthermore, qRT-PCR analyses revealed that the PnTLP members were up-regulated or down-regulated in response to F. solani stress. The results of this study provide insight into the PnTLP gene family, and their potential biological functions in plants' defenses against pathogenic fungi, which would provide candidate genes for future studies of their roles in disease resistance.

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“…This protectant mechanism has also been observed in the cultivated watermelon ( Yuan et al., 2022a ; Yuan et al., 2022b ) where it aided the crop to survive against the drought and salinity stresses. Other important molecular mechanisms that has shown potential to play an important role in the tolerance mechanisms of citrullus species is the Thaumatin-like protein (TLP) that has been documented to be actively involved in responses abiotic stresses in watermelon ( Ram et al., 2022 ). All these potential tolerance mechanisms as observed in cultivated watermelon could thus suggest a much more pronounced expression and role in the more tolerant wild watermelon.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Drought stress tolerance mechanisms and their potential common indicators to salinity, insights from the wild watermelon (Citrullus lanatus): A review

Malambane

Madumane²,

Sewelo³

et al. 2023

Front. Plant Sci.

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Climate change has escalated the effect of drought on crop production as it has negatively altered the environmental condition. Wild watermelon grows abundantly in the Kgalagadi desert even though the environment is characterized by minimal rainfall, high temperatures and intense sunshine during growing season. This area is also characterized by sandy soils with low water holding capacity, thus bringing about drought stress. Drought stress affects crop productivity through its effects on development and physiological functions as dictated by molecular responses. Not only one or two physiological process or genes are responsible for drought tolerance, but a combination of various factors do work together to aid crop tolerance mechanism. Various studies have shown that wild watermelon possess superior qualities that aid its survival in unfavorable conditions. These mechanisms include resilient root growth, timely stomatal closure, chlorophyll fluorescence quenching under water deficit as key physiological responses. At biochemical and molecular level, the crop responds through citrulline accumulation and expression of genes associated with drought tolerance in this species and other plants. Previous salinity stress studies involving other plants have identified citrulline accumulation and expression of some of these genes (chloroplast APX, Type-2 metallothionein), to be associated with tolerance. Emerging evidence indicates that the upstream of functional genes are the transcription factor that regulates drought and salinity stress responses as well as adaptation. In this review we discuss the drought tolerance mechanisms in watermelons and some of its common indicators to salinity at physiological, biochemical and molecular level.

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Genome-wide comprehensive characterization and expression analysis of TLP gene family revealed its responses to hormonal and abiotic stresses in watermelon (Citrullus lanatus)

Cited by 12 publications

References 101 publications

Genome wide comprehensive characterization and expression analysis of RBOH genes revealed drought stress response in mung bean (Vigna radiate L.)

Genome wide comprehensive characterization and expression analysis of RBOH genes revealed drought stress response in mung bean (Vigna radiate L.)

Genome-wide identification of thaumatin-like protein family genes in Panax notoginseng and analysis of their responses to Fusarium solani infection

Drought stress tolerance mechanisms and their potential common indicators to salinity, insights from the wild watermelon (Citrullus lanatus): A review

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