In silico analysis of ESTs from roots of Rangpur lime (Citrus limonia Osbeck) under water stress

Boscariol-Camargo, Raquel L.; Berger, Irving Joseph; Souza, Alessandra Alves de; Amaral, Alexandre Morais do; Carlos, Eduardo Fermino; Freitas-Astúa, Juliana; Takita, Marco Aurélio; Targon, M. L. P. N.; Medina, Camilo Lázaro; Reis, Marcelo S.; Machado, Marcos Antônio

doi:10.1590/s1415-47572007000500019

Cited by 22 publications

(9 citation statements)

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“…The reliability of our transcriptomic data was supported by detection of 41,827 (94.2%) unique transcripts out of 44,387 currently known sweet orange transcripts [27], and by the results of qPCR analysis (Table 1). They revealed a total of 1764 transcripts showing significant variation of expression in response to the drought stress conditions tested, which is far higher than in the previous studies [20, 21]. Our results show that the fraction of the sweet orange transcriptome regulated by drought stress is relatively small (4.2%), mostly represented by upregulated genes (61.3%) and functionally diverse (Figs.…”

Section: Discussioncontrasting

confidence: 58%

“…2b and Additional file 5: Table S4). HSPs, ERDs, PMTs and miraculin are some of the well kwown gene products involved in the stress cellular responses in citrus and other plants [20, 21, 39, 40].…”

Section: Discussionmentioning

confidence: 99%

“…The response of citrus to drought stress is poorly understood at molecular level. In a first attempt, expressed-sequence-tag (EST) analysis of 4130 valid reads from roots of ‘Rangpur’ seedlings cultivated in hydroponic conditions with and without drought stress using polyethylene glycol-6000 (PEG-6000) resulted in the identification of 40 differentially expressed genes [20]. These included homologues to well known genes involved in drought-stress response, such as aquaporins, chaperones, dehydrin, proteases, sucrose synthase and proline-related synthase, as well as homologues to other previously unrelated genes involved with cell energy [e.g.…”

Section: Introductionmentioning

confidence: 99%

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Rootstock-induced molecular responses associated with drought tolerance in sweet orange as revealed by RNA-Seq

Gonçalves

Boscariol-Camargo²,

Takita³

et al. 2019

BMC Genomics

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BackgroundCitrus plants are commercially propagated by grafting, with the rootstock variety influencing a number of horticultural traits, including drought tolerance. Among the different rootstock varieties available for citrus propagation, ‘Rangpur’ lime is known to confer enhanced tolerance to drought as compared to other citrus rootstocks. The objective of this study was to investigate the poorly understood molecular responses underlying the rootstock-induced drought tolerance in sweet orange.ResultsRNA-Seq transcriptome analysis was carried out in leaves of sweet orange grafted on ‘Rangpur’ lime subjected to control and drought-stress treatments, under greenhouse conditions, using the Illumina HiSeq platform. A total of 41,827 unique transcripts were identified, among which 1764 transcripts showed significant variation (P ≤ 0.001) between the treatments, with 1081 genes induced and 683 repressed by drought-stress treatment. The transcripts were distributed in 44 different categories of cellular component, molecular function and biological process. Several genes related to cell metabolism, including those involved in the metabolisms of cell wall, carbohydrates and antioxidants, light reactions, biotic and abiotic stress responses, as well as genes coding for transcription factors (TFs), protein kinases (PKs) and proteins involved in the abscisic acid (ABA) and ethylene signaling pathways, were differentially regulated by drought stress. RNA-Seq data were validated by quantitative real-time PCR (qPCR) analysis and comparative analysis of expression of the selected genes between sweet orange grafted on drought-tolerant and -sensitive rootstocks revealed new candidate genes for drought tolerance in citrus.ConclusionsIn conclusion, our results showed that only a relatively small but functionally diverse fraction of the sweet orange transcriptome, with functions in metabolism, cellular responses and regulation, was differentially regulated by drought stress. The data suggest that the rootstock-induced drought tolerance in sweet orange includes the transcriptional activation of genes related to the cell wall, soluble carbohydrate and antioxidant metabolisms, biotic and abiotic stress responses, TFs, PKs and ABA signaling pathway, and the downregulation of genes involved in the starch metabolism, light reactions and ethylene signaling. Future efforts to elucidate their functional roles and explore their potential in the citrus genetic improvement should benefit from this data.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5481-z) contains supplementary material, which is available to authorized users.

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Section: Discussioncontrasting

confidence: 58%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Rootstock-induced molecular responses associated with drought tolerance in sweet orange as revealed by RNA-Seq

Gonçalves

Boscariol-Camargo²,

Takita³

et al. 2019

BMC Genomics

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“…Spot 1 showed identity with chaperonin‐21. This protein has been shown to assist proteins such as Rubisco and cause up‐regulation of the chaperonin‐21 gene under water stress in Rangpur lime roots (Boscariol‐Camargo et al. 2007).…”

Section: Resultsmentioning

confidence: 99%

Water stress induces up‐regulation of DOF1 and MIF1 transcription factors and down‐regulation of proteins involved in secondary metabolism in amaranth roots (Amaranthus hypochondriacus L.)

et al. 2010

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Roots are the primary sites of water stress perception in plants. The aim of this work was to study differential expression of proteins and transcripts in amaranth roots (Amaranthus hypochondriacus L.) when the plants were grown under drought stress. Changes in protein abundance within the roots were examined using two-dimensional electrophoresis and LC/ESI-MS/MS, and the differential expression of transcripts was evaluated with suppression subtractive hybridisation (SSH). Induction of drought stress decreased relative water content in leaves and increased solutes such as proline and total soluble sugars in roots. Differentially expressed proteins such as SOD(Cu-Zn) , heat shock proteins, signalling-related and glycine-rich proteins were identified. Up-regulated transcripts were those related to defence, stress, signalling (Ser, Tyr-kinases and phosphatases) and water transport (aquaporins and nodulins). More noteworthy was identification of the transcription factors DOF1, which has been related to several plant-specific biological processes, and MIF1, whose constitutive expression has been related to root growth reduction and dwarfism. The down-regulated genes/proteins identified were related to cell differentiation (WOX5A) and secondary metabolism (caffeic acid O-methyltransferase, isoflavone reductase-like protein and two different S-adenosylmethionine synthetases). Amaranth root response to drought stress appears to involve a coordinated response of osmolyte accumulation, up-regulation of proteins that control damage from reactive oxygen species, up-regulation of a family of heat shock proteins that stabilise other proteins and up-regulation of transcription factors related to plant growth control.

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“…Transcriptomic studies have revealed that the expression of a wide range of genes is regulated in response to water deficit in citrus plants. Analysis of 2,100 expressed sequence tags (ESTs) in the roots of Rangpur lime ( Citrus limonia Osbeck) subjected to osmotic stress resulted in the identification of genes involved in the water stress response, including those encoding aquaporins, dehydrins, sucrose synthase and enzymes related to the synthesis of proline [ 6 ]. Using a microarray containing 6,000 genes, Gimeno et al .…”

Section: Introductionmentioning

confidence: 99%

Comparative study of the protein profiles of Sunki mandarin and Rangpur lime plants in response to water deficit

et al. 2015

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BackgroundRootstocks play a major role in the tolerance of citrus plants to water deficit by controlling and adjusting the water supply to meet the transpiration demand of the shoots. Alterations in protein abundance in citrus roots are crucial for plant adaptation to water deficit. We performed two-dimensional electrophoresis (2-DE) separation followed by LC/MS/MS to assess the proteome responses of the roots of two citrus rootstocks, Rangpur lime (Citrus limonia Osbeck) and ‘Sunki Maravilha’ (Citrus sunki) mandarin, which show contrasting tolerances to water deficits at the physiological and molecular levels.ResultsChanges in the abundance of 36 and 38 proteins in Rangpur lime and ‘Sunki Maravilha’ mandarin, respectively, were observed via LC/MS/MS in response to water deficit. Multivariate principal component analysis (PCA) of the data revealed major changes in the protein profile of ‘Sunki Maravilha’ in response to water deficit. Additionally, proteomics and systems biology analyses allowed for the general elucidation of the major mechanisms associated with the differential responses to water deficit of both varieties. The defense mechanisms of Rangpur lime included changes in the metabolism of carbohydrates and amino acids as well as in the activation of reactive oxygen species (ROS) detoxification and in the levels of proteins involved in water stress defense. In contrast, the adaptation of ‘Sunki Maravilha’ to stress was aided by the activation of DNA repair and processing proteins.ConclusionsOur study reveals that the levels of a number of proteins involved in various cellular pathways are affected during water deficit in the roots of citrus plants. The results show that acclimatization to water deficit involves specific responses in Rangpur lime and ‘Sunki Maravilha’ mandarin. This study provides insights into the effects of drought on the abundance of proteins in the roots of two varieties of citrus rootstocks. In addition, this work allows for a better understanding of the molecular basis of the response to water deficit in citrus. Further analysis is needed to elucidate the behaviors of the key target proteins involved in this response.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0416-6) contains supplementary material, which is available to authorized users.

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In silico analysis of ESTs from roots of Rangpur lime (Citrus limonia Osbeck) under water stress

Cited by 22 publications

References 85 publications

Rootstock-induced molecular responses associated with drought tolerance in sweet orange as revealed by RNA-Seq

Rootstock-induced molecular responses associated with drought tolerance in sweet orange as revealed by RNA-Seq

Water stress induces up‐regulation of DOF1 and MIF1 transcription factors and down‐regulation of proteins involved in secondary metabolism in amaranth roots (Amaranthus hypochondriacus L.)

Comparative study of the protein profiles of Sunki mandarin and Rangpur lime plants in response to water deficit

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