Genome-wide identification, structure analysis and expression profiling of phospholipases D under hormone and abiotic stress treatment in chickpea (Cicer arietinum)

Sagar, Sushma; Deepika,; Biswas, Dipul Kumar; Chandrasekar, Ramsankar; Singh, Amarjeet

doi:10.1016/j.ijbiomac.2020.12.102

Cited by 25 publications

(16 citation statements)

References 55 publications

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“…Each clade of PLDs in the phylogenetic tree have revealed similar motif distribution and exon-intron structure which further indicated that the PLD structure was conserved in each group. Similar exon-intron structure for each group of PLD genes has also been reported in other plants including Arabidopsis (Qin and Wang 2002), soybean (Zhao et al 2012), rice (Li et al 2007), chickpea (Sagar et al 2021), and rapeseed (Lu et al 2019). The relation between the intron phase and the degree of conservation at splicing site sequence is correlated with the evolution of spliceosomal introns.…”

Section: Discussionsupporting

confidence: 70%

Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea (Camellia sinensis)

Roshan

Ashouri

Sadeghi

2021

Physiol Mol Biol Plants

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Phospholipase D (PLD) (EC 3.1.4.4) plays important roles in plants growth, development, and response to environmental stresses. Tea plant (Camellia sinensis) is the most important non-alcoholic beverage in the world with health benefits, but tea production decreases in response to environmental stresses such as cold and drought. Therefore, a genome-wide analysis of the C. sinensis PLD gene family (CsPLDs) was carried out. In the current study, identification, evolutionary relationship, duplication, selection pressure, gene structure, promoter analysis, transcript-targeted miRNA, and simple sequence repeat markers prediction, RNA-seq data analysis, and three-dimensional structure of the CsPLDs have been investigated using bioinformatics tools. 15 PLDs were identified from the tea genome which belongs to five groups, including CsPLDa, CsPLDb, CsPLDd, CsPLDe, and CsPLDf. Both segmental and tandem duplications have occurred in the CsPLD gene family. Ka/Ks ratio for the most duplicated pair genes was less than 1 which implies negative selection to conserve their function during the tea evolution. 68 cis-elements have been found in CsPLDs indicating the contribution of these genes in response to environmental stresses. Likewise, 72 SSR loci and 96 miRNA molecules in 14 and 15 CsPLDs have been detected. According to RNA-seq data, the highest expression in all tissues under various abiotic stresses was related to CsPLDa1. Besides, a three-dimensional structure of the CsPLDa1 was evaluated to better understand its biological activity. This research provides comprehensive information that could be useful in future studies to develop stresstolerant tea.

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Section: Discussionsupporting

confidence: 70%

Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea (Camellia sinensis)

Roshan

Ashouri

Sadeghi

2021

Physiol Mol Biol Plants

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“…The PLD gene family has been identified in many species, including 12 in Arabidopsis thaliana [ 22 ], 17 in Oryza sativa [ 12 ], 19 in Gossypium [ 35 ], 13 in Zea mays [ 3 ], and 13 in Cicer arietinum [ 14 ]. This experiment identified 16 PLD genes in the potato genome, all of which contained HxKxxxxD conserved motifs, with molecular weights ranging from 86.96 kDa to 126.22 kDa ( Table 1 ).…”

Section: Discussionmentioning

confidence: 99%

“…The quantitative results under drought stress showed that not only the genes of the PLDα subfamily were significantly upregulated, but the genes of other sub-families were also significantly upregulated, indicating that other sub-families are also involved in the process of stomata opening and closing [ 47 ]. Studies have shown that chickpea PLD [ 14 ] genes are exclusively upregulated in the upper part of the ground under drought stress, indicating that they may play a role in the closure of stomata, thereby reducing transpiration and water loss. Prior to this, PLD has been thought to regulate stomata closure under drought and hypertonic stress [ 48 , 49 ].…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Analysis and Expression Profiling of the Phospholipase D Gene Family in Solanum tuberosum

Zhang

et al. 2021

Biology

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Phospholipase D (PLD) is the most important phospholipid hydrolase in plants, which can hydrolyze phospholipids into phosphatidic acid (PA) and choline. When plants encounter low temperature, drought and high salt stress, phospholipase D and its products play an important role in regulating plant growth and development and coping with stress. In this study, 16 members of StPLD gene family were identified in potato genome, which were distributed in α, β, δ, and ζ subfamilies, and their expression patterns under salt, high temperature, drought, and ABA stress were detected by qRT-PCR method. Gene expression analysis showed that the expression of StPLD genes in potato was upregulated and downregulated to varying degrees under the four stresses, indicating that the PLD gene family is involved in the interaction of potato plant hormones and abiotic stress signals. Chromosome distribution showed that StPLD gene was unevenly distributed on 8 chromosomes, and only one pair of tandem repeat genes was found. All StPLD promoters contain hormone and stress-related cis-regulatory elements to respond to different stresses. Structural analysis showed that StPLD genes in the same subgroup had a similar exon–intron structure. Our study provides a valuable reference for further research of the function and structure of PLD gene.

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“…Three biological replicate samples (with three technical replicates of each biological replicate) of control and nutrient-deficient root and shoots were used to assess the expression pattern. iTaq Universal SYBR Green supermix (Bio-Rad) was used to detect the expression in Bio-rad CFX96 real-time PCR system (Bio-Rad) according to Sagar et al ( 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Molecular Characterization Reveals the Involvement of Calcium Dependent Protein Kinases in Abiotic Stress Signaling and Development in Chickpea (Cicer arietinum)

et al. 2022

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Calcium-dependent protein kinases (CDPKs) are a major group of calcium (Ca2+) sensors in plants. CDPKs play a dual function of “Ca2+ sensor and responder.” These sensors decode the “Ca2+ signatures” generated in response to adverse growth conditions such as drought, salinity, and cold and developmental processes. However, knowledge of the CDPK family in the legume crop chickpea is missing. Here, we have identified a total of 22 CDPK genes in the chickpea genome. The phylogenetic analysis of the chickpea CDPK family with other plants revealed their evolutionary conservation. Protein homology modeling described the three-dimensional structure of chickpea CDPKs. Defined arrangements of α-helix, β-strands, and transmembrane-helix represent important structures like kinase domain, inhibitory junction domain, N and C-lobes of EF-hand motifs. Subcellular localization analysis revealed that CaCDPK proteins are localized mainly at the cytoplasm and in the nucleus. Most of the CaCDPK promoters had abiotic stress and development-related cis-regulatory elements, suggesting the functional role of CaCDPKs in abiotic stress and development-related signaling. RNA sequencing (RNA-seq) expression analysis indicated the role of the CaCDPK family in various developmental stages, including vegetative, reproductive development, senescence stages, and during seed stages of early embryogenesis, late embryogenesis, mid and late seed maturity. The real-time quantitative PCR (qRT-PCR) analysis revealed that several CaCDPK genes are specifically as well as commonly induced by drought, salt, and Abscisic acid (ABA). Overall, these findings indicate that the CDPK family is probably involved in abiotic stress responses and development in chickpeas. This study provides crucial information on the CDPK family that will be utilized in generating abiotic stress-tolerant and high-yielding chickpea varieties.

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Genome-wide identification, structure analysis and expression profiling of phospholipases D under hormone and abiotic stress treatment in chickpea (Cicer arietinum)

Cited by 25 publications

References 55 publications

Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea (Camellia sinensis)

Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea (Camellia sinensis)

Genome-Wide Analysis and Expression Profiling of the Phospholipase D Gene Family in Solanum tuberosum

Molecular Characterization Reveals the Involvement of Calcium Dependent Protein Kinases in Abiotic Stress Signaling and Development in Chickpea (Cicer arietinum)

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