Javier Canales

Javier Canales
Universidad Austral de Chile · Instituto de Bioquímica & Microbiología

Biologist, PhD

About

58
Publications
9,541
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Introduction
Our research is focused on the molecular mechanisms underlying the response of plants to nutrients, specifically, on the complex interactions between nutrients in metabolic pathways. On our research we use a combination of bioinformatics, transcriptomics, molecular biology and plant physiology approaches. https://ngp-lab.com/
Additional affiliations
October 2012 - March 2015
Pontificia Universidad Católica de Chile
Position
  • PostDoc Position
June 2005 - November 2011
University of Malaga
Position
  • PhD Student

Publications

Publications (58)
Article
Root hairs are specialized cells important for nutrient uptake. It is well established that nutrients such as phosphate have great influence on root hair development in many plant species. Here, we investigated the role of nitrate on root hair development at a physiological and molecular level. We showed nitrate increase root hair density in Arabid...
Article
Sulfur is an essential nutrient for plant growth and development. Sulfur is a constituent of proteins, the plasma membrane and cell walls, among other important cellular components. To obtain new insights into the gene regulatory networks underlying the sulfate response, we performed an integrative meta-analysis of transcriptomic data from five dif...
Article
Full-text available
Background: Sulfur is a major component of biological molecules and thus an essential element for plants. Deficiency of sulfate, the main source of sulfur in soils, negatively influences plant growth and crop yield. The effect of sulfate deficiency on plants has been well characterized at the physiological, transcriptomic and metabolomic levels in...
Article
Full-text available
A critical barrier to improving crop yield is the trade-off between seed weight (SW) and seed number (SN), which has been commonly reported in several crops, including Brassica napus. De-spite the agronomic relevance of this issue, the molecular factors involved in the interaction be-tween SW and SN are largely unknown in crops. In this work, we pe...
Article
Full-text available
LSU proteins belong to a plant-specific gene family initially characterized by their strong induction in response to sulfate (S) deficiency. In the last few years, LSUs have arisen as relevant hubs in protein–protein interaction networks, in which they play relevant roles in the response to abiotic and biotic stresses. Most of our knowledge on LSU...
Preprint
Full-text available
LSU (RESPONSE TO LOW SULFUR) proteins belong to a plant-specific gene family initially characterized by their strong induction in response to sulfate (S) deficiency. However, little is known about the LSU gene repertoire and evolution of this family in land plants. In this work, a total of 270 LSU family members were identified using 134 land plant...
Article
Full-text available
Perennial ryegrass (Lolium perenne L.) possesses a high level of nutritional quality and is widely used as a forage species to establish permanent pastures in southern Chile. However, the productivity of most such pastures is limited by various environmental agents, such as insect pests and drought. In this context, our work stresses the need for e...
Article
Full-text available
The potato (Solanum tuberosum L.) is the fourth most important crop for global food security. Its tubers contain high concentrations of antioxidants, especially in genotypes with red or purple pigmentation. The Potato Genebank of the Universidad Austral of Chile includes accessions that show pigmentation in their flesh and/or skin as well as high l...
Article
Full-text available
In a changing climate, extreme weather events such as heatwaves will be more frequent and could affect grain weight and the quality of crops such as wheat, one of the most significant crops in terms of global food security. In this work, we characterized the response of Triticum turgidum L. spp. durum wheat to short-term heat stress (HS) treatment...
Preprint
Full-text available
In a changing climate, extreme weather events such as heat waves will be more frequent and could affect grain weight and the quality of crops such as wheat, one of the most significant crops in terms of global food security. In this work, we characterized the response of Triticum turgidum spp. durum wheat to a short-term heat-stress (HS) treatment...
Article
Full-text available
The development of high nitrogen use efficiency (NUE) cultivars under low N inputs is required for sustainable agriculture. To this end, in this study, we analyzed the impact of long-term suboptimal N conditions on the metabolome and transcriptome of tomato to identify specific molecular processes and regulators at the organ scale. Physiological an...
Article
Full-text available
Nitrate is an essential macronutrient and a signal molecule that regulates the expression of multiple genes involved in plant growth and development. Here we describe the participation of Arabidopsis DOF transcription factor CDF3 in nitrate responses and show that CDF3 gene is induced under nitrate starvation. Moreover, knockout cdf3 mutant plants...
Preprint
Full-text available
Background: Sulfur (S) is a major component of biological molecules and thus an essential element for plants. Although the biochemistry and metabolism of sulfate is well understood, little is known about the regulatory mechanisms underlying plant responses to sulfate deprivation, especially in crop plants such as tomato (Solanum lycopersicum). In t...
Preprint
Full-text available
Background: Sulfur is a major component of biological molecules and thus an essential element for plants. Deficiency of sulfate, the main source of sulfur in soils, negatively influences plant growth and crop yield. The effect of sulfate deficiency on plants has been well characterized at the physiological, transcriptomic and metabolomic levels in...
Preprint
Full-text available
Background: Sulfur is a major component of biological molecules and thus an essential element for plants. Deficiency of sulfate, the main source of sulfur in soils, negatively influences plant growth and crop yield. The effect of sulfate deficiency on plants has been well characterized at the physiological, transcriptomic and metabolomic levels in...
Article
Precise coordination of cell expansion and cell proliferation underlies growth in multicellular organisms. In addition to endogenous developmental programs, external environmental signals are integrated to modulate organ growth in plants. Nitrate is a nitrogen nutrient that can act as a potent signal to modulate shoot growth, yet the molecular mech...
Article
Full-text available
Background: Grain weight (GW) is a key component of sunflower yield and quality, but may be limited by maternal tissues. Cell growth is influenced by expansin proteins that loosen the plant cell wall. This study aimed to identify spatio-temporal expression of EXPN genes in sunflower reproductive organ tissues (ovary, pericarp, and embryo) and evalu...
Data
List of genes involved in the sulfate co-expression network ranked according to their number of connections.
Data
qPCR analysis of genes that are related to sulfate assimilation and that belong to module M1 of the sulfate co-expression network. For details, see the legend in Figure 2. Student’s t-test was performed to test the significant differences (p < 0.05) between FN and +/-S treatments. Significant changes are indicated with an asterisk.
Data
Venn diagram showing the genes shared between nitrate- and sulfate-responsive genes. For this analysis, we considered only genes reported as differentially expressed in at least two different experiments in a previous study (Canales et al., 2014) or in the present study.
Data
Selection of the Pearson’s correlation threshold for the construction of the sulfate co-expression network.
Data
List of oligonucleotides used for qPCR analyses.
Data
List of sulfate-responsive genes ranked according to their consistency in the sulfate response.
Data
Overlap between genes and GO terms in our meta-analysis and the pioneering microarray experiments of Hirai et al. (2003), Nikiforova et al. (2003), and Maruyama-Nakashita et al. (2006).
Data
Gene Expression Omnibus accession numbers and descriptions of the samples included in Figure 4B.
Article
Full-text available
Plants have developed different signaling systems allowing for the integration of environmental cues to coordinate molecular processes associated to both early development and the physiology of the adult plant. Research on systemic signaling in plants has traditionally focused on the role of phytohormones as long-distance signaling molecules, and m...
Article
GENIUS is a user-friendly web server that uses a novel machine learning algorithm to infer functional gene networks focused on specific genes and experimental conditions that are relevant to biological functions of interest. These functions may have different levels of complexity, from specific biological processes to complex traits that involve se...
Article
Full-text available
Nitrogen is one of the most important nutrients for plants and, in natural soils, its availability is often a major limiting factor for plant growth. Here we examine the effect of different forms of nitrogen nutrition and of photorespiration on gene expression in the model legume Lotus japonicus with the aim of identifying regulatory candidate gene...
Article
Nitrogen (N) is one of the main limiting nutrients for plant growth and crop yield. It is well documented that changes in nitrate availability, the main N source found in agricultural soils, influences a myriad of developmental programs and processes including the plant defense response. Indeed, many agronomical reports indicate that the plant N nu...
Article
Full-text available
PpDof 5 is a regulator of the expression of glutamine synthetase (GS; EC 6.3.1.2) genes in photosynthetic and non-photosynthetic tissues of maritime pine. We have used Arabidopsis thaliana as a model system to study PpDof 5 function in planta, generating transgenic lines overexpressing the pine transcription factor. The overexpression of PpDof 5 re...
Article
Full-text available
The utilization of high amounts of nitrate fertilizers for crop yield leads to nitrate pollution of ground and surface waters. In this paper, we report the assimilation and utilization of nitrate luxuriant levels, 20 times more than the highest N fertilizer application in Europe, by transgenic poplars overexpressing a cytosolic glutamine synthetase...
Article
Full-text available
Conifers include long-lived evergreen trees of great economic and ecological importance, including pines and spruces. During their long lives conifers must respond to seasonal environmental changes, adapt to unpredictable environmental stresses, and co-ordinate their adaptive adjustments with internal developmental programmes. To gain insights into...
Article
Nitrogen (N) is an essential macronutrient and a key structural component of macromolecules in plants. N nutrients and metabolites can act as signals that impact on many aspects of plant biology. The plant life cycle involves a series of developmental phase transitions that must be tightly coordinated to external and internal cues in order to ensur...
Article
Full-text available
Nitrogen (N) is an essential macronutrient for plant growth and development. Plants adapt to changes in N availability partly by changes in global gene expression. We integrated publicly available root microarray data under contrasting nitrate conditions to identify new genes and functions important for adaptive nitrate responses in Arabidopsis tha...
Article
Full-text available
Maritime pine (Pinus pinaster Aiton) is one of the most advanced conifer models for genomics research. Conifer genomes are extremely large and major advances have recently been made in the characterization of transcriptomes. The combination of laser capture microdissection (LCM) and next-generation sequencing is a powerful tool with which to resolv...
Article
Full-text available
Maritime pine (Pinus pinasterAit.) is a widely distributed conifer species in Southwestern Europe and one of the most advanced models for conifer research. In the current work, comprehensive characterization of the maritime pine transcriptome was performed using a combination of two different next-generation sequencing platforms, 454 and Illumina....
Article
Ectomycorrhizal associations are of major ecological importance in temperate and boreal forests. The development of a functional ectomycorrhiza requires many genetic and biochemical changes. In this study, suppressive subtraction hybridization was used to identify differentially expressed genes in the roots of maritime pine (Pinus pinaster Aiton) i...
Conference Paper
Full-text available
Forest trees dominate large ecosystems and include a broad variety of plant species, some ranking as the largest, tallest, and longest living organisms on Earth. Conifers are the most important group of gymnosperms, which include tree species of great ecological and economic importance that dominate large ecosystems and play an essential role in gl...
Article
Full-text available
Asparagine, a key amino acid for nitrogen storage and transport in plants, is synthesized via the ATP-dependent reaction catalyzed by the enzyme asparagine synthetase (AS; EC 6.3.5.4). In this work, we present the molecular analysis of two full-length cDNAs that encode asparagine synthetase in maritime pine (Pinus pinaster Ait.), PpAS1, and PpAS2....
Article
Full-text available
The shoots of young conifer trees represent an interesting model to study the development and growth of conifers from meristematic cells in the shoot apex to differentiated tissues at the shoot base. In this work, microarray analysis was used to monitor contrasting patterns of gene expression between the apex and the base of maritime pine shoots. A...
Data
Principal Component Analysis (PCA) of GS genes and genes involved in lignin biosynthesis and C1 metabolism. The expression profiles of GS genes were examined in silico during wood formation in hybrid poplar (Populus tremula x Populus tremuloides) using the microarray data available in Populus DB [48]. Tissue samples were collected from five positio...
Data
Predicted and sequenced cDNAs of poplar GS genes. Predicted and sequenced cDNAs of poplar GS genes are listed.
Article
Full-text available
Glutamine synthetase (GS; EC: 6.3.1.2, L-glutamate: ammonia ligase ADP-forming) is a key enzyme in ammonium assimilation and metabolism of higher plants. The current work was undertaken to develop a more comprehensive understanding of molecular and biochemical features of GS gene family in poplar, and to characterize the developmental regulation of...
Article
Full-text available
Pinus pinaster is an economically and ecologically important species that is becoming a woody gymnosperm model. Its enormous genome size makes whole-genome sequencing approaches are hard to apply. Therefore, the expressed portion of the genome has to be characterised and the results and annotations have to be stored in dedicated databases. EuroPine...
Article
A large family of small cysteine-rich antimicrobial peptides (AMPs) is involved in the innate defence of plants against pathogens. Recently, it has been shown that AMPs may also play important roles in plant growth and development. In previous work, we have identified a gene of the AMP β-barrelin family that was differentially regulated in the root...
Article
Full-text available
Conifers have a preference for ammonium over nitrate as the main inorganic nitrogen source. However, it is unknown how changes in nitrogen nutrition may affect transcription profiles. In this study, microarray analysis and suppressive subtraction hybridization were used to identify differentially expressed genes in the roots of maritime pine expose...

Projects

Projects (5)
Project
The objective of this project is to improve the knowledge of physiological mechanisms and key genes controlling the determination of GN, GW, their interaction and grain quality of wheat in key and unique genotypes (transgenic and triple-mutant wheats)under contrasting management (plant density) and climatic (locations) conditions. The determinations of GN and GW overlap from booting to 10 days after anthesis. This overlapping is seen in this project as the key to unlock the understanding of the GW-GN trade-off as well as the key and unique genotypes.
Project
Lowering fertilizer inputs and breeding plants with better nitrogen use efficiency (NUE) is one of the main goals of research on plant nutrition to sustainable production and environment (Hirel et al., 2007). Nevertheless, NUE in plants is a complex process encompassing many physiological processes including nitrogen uptake, assimilation, metabolism, storage, partition, allocation and remobilization.
Project
Dear Colleagues, In the past twenty years, our knowledge about whole genome sequences of plants has increased extraordinarily, and now, there are around 400 whole genome assemblies of seed plants in the NCBI databases. However, this information is only the first step toward understanding the life complexity at a molecular level. In this context, functional genomics has become fundamental in biological research. In a broad sense, it is a very extensive research area including from genome functional annotation to metabolome passing through to gene expression regulation. The omics techniques associated to this discipline are accelerating the pace with which we obtain new knowledge about crops and about to how improve them through biotechnological techniques. The objective of this Special Issue is to present to the international research community a wide perspective about functional genomics in crops (including herbaceous and tree species). Submissions on the main topics are invited, but not excluding other related topics: (1) Omics works in transcriptomics, proteomics and metabolomics but even in epigenomics and epitranscriptomics; (2) Gene expression regulation, including transcription but also translation; (3) Protein–protein and protein–nucleic acid interactions; (4) Mutagenesis and gene edition (RNAi, CRISPR, etc.); (5) Bioinformatic tools for functional genomics including genome annotation, direct RNA sequencing, etc.; (6) Any work on functional genomics in crops.