Publications by authors named "Herman Silva"

33 Publications

A de novo transcriptome analysis revealed that photomorphogenic genes are required for carotenoid synthesis in the dark-grown carrot taproot.

Mol Genet Genomics 2020 Nov 12;295(6):1379-1392. Epub 2020 Jul 12.

Facultad de Ciencias, Centro de Biología Molecular Vegetal, Universidad de Chile, Las Palmeras, 3425, Ñuñoa, Santiago, Chile.

Carotenoids are terpenoid pigments synthesized by all photosynthetic and some non-photosynthetic organisms. In plants, these lipophilic compounds are involved in photosynthesis, photoprotection, and phytohormone synthesis. In plants, carotenoid biosynthesis is induced by several environmental factors such as light including photoreceptors, such as phytochromes (PHYs) and negatively regulated by phytochrome interacting factors (PIFs). Daucus carota (carrot) is one of the few plant species that synthesize and accumulate carotenoids in the storage root that grows in darkness. Contrary to other plants, light inhibits secondary root growth and carotenoid accumulation suggesting the existence of new mechanisms repressed by light that regulate both processes. To identify genes induced by dark and repressed by light that regulate carotenoid synthesis and carrot root development, in this work an RNA-Seq analysis was performed from dark- and light-grown carrot roots. Using this high-throughput sequencing methodology, a de novo transcriptome model with 63,164 contigs was obtained, from which 18,488 were differentially expressed (DEG) between the two experimental conditions. Interestingly, light-regulated genes are preferably expressed in dark-grown roots. Enrichment analysis of GO terms with DEGs genes, validation of the transcriptome model and DEG analysis through qPCR allow us to hypothesize that genes involved in photomorphogenesis and light perception such as PHYA, PHYB, PIF3, PAR1, CRY2, FYH3, FAR1 and COP1 participate in the synthesis of carotenoids and carrot storage root development.
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http://dx.doi.org/10.1007/s00438-020-01707-4DOI Listing
November 2020

RNA-seq Analysis of Salt-Stressed Non Salt-Stressed Transcriptomes of Landrace R49.

Genes (Basel) 2019 12 16;10(12). Epub 2019 Dec 16.

Departamento de Producción Agrícola, Laboratorio de Genómica Funcional y Bioinformática, Universidad de Chile, Av. Santa Rosa 11315, Santiago 8820808, Chile.

Quinoa ( Willd.), a model halophytic crop species, was used to shed light on salt tolerance mechanisms at the transcriptomic level. An RNA-sequencing analysis of genotype R49 at an early vegetative stage was performed by Illumina paired-ends method comparing high salinity and control conditions in a time-course pot experiment. Genome-wide transcriptional salt-induced changes and expression profiling of relevant salt-responsive genes in plants treated or not with 300 mM NaCl were analyzed after 1 h and 5 days. We obtained up to 49 million pairs of short reads with an average length of 101 bp, identifying a total of 2416 differentially expressed genes (DEGs) based on the treatment and time of sampling. In salt-treated vs. control plants, the total number of up-regulated and down-regulated genes was 945 and 1471, respectively. The number of DEGs was higher at 5 days than at 1 h after salt treatment, as reflected in the number of transcription factors, which increased with time. We report a strong transcriptional reprogramming of genes involved in biological processes like oxidation-reduction, response to stress and response to abscisic acid (ABA), and cell wall organization. Transcript analyses by real-time RT- qPCR supported the RNA-seq results and shed light on the contribution of roots and shoots to the overall transcriptional response. In addition, it revealed a time-dependent response in the expression of the analyzed DEGs, including a quick (within 1 h) response for some genes, suggesting a "stress-anticipatory preparedness" in this highly salt-tolerant genotype.
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http://dx.doi.org/10.3390/genes10121042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6947843PMC
December 2019

Transcriptome datasets from leaves and fruits of the sweet cherry cultivars 'Bing', 'Lapins' and 'Rainier'.

Data Brief 2019 Apr 22;23:103696. Epub 2019 Jan 22.

Universidad de Chile, Facultad de Ciencias Agronómicas, Departamento de Producción Agrícola, Laboratorio de Genómica Funcional, & Bioinformática, 820808 La Pintana, Santiago, Chile.

Sweet cherry fruits from different cultivars have different pre- and post-harvest qualities. Here we present the transcriptome profile datasets of leaves and mature fruits of three sweet cherry cultivars ('Bing', 'Lapin' and 'Rainier'). Using 454 GS-FLX technology (454 Life Sciences, Roche), transcriptomes of leaves and mature fruits were obtained from these cultivars. These transcriptome data sets are reported here.
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http://dx.doi.org/10.1016/j.dib.2019.01.044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369327PMC
April 2019

Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling.

PLoS One 2018 3;13(12):e0208032. Epub 2018 Dec 3.

Universidad de Chile, Facultad de Ciencias Agronómicas, Departamento de Producción Agrícola, Laboratorio de Genómica Funcional & Bioinformática, La Pintana, Santiago, Chile.

This study reports the construction of high density linkage maps of Japanese plum (Prunus salicina Lindl.) using single nucleotide polymorphism markers (SNPs), obtained with a GBS strategy. The mapping population (An x Au) was obtained by crossing cv. "Angeleno" (An) as maternal line and cv. "Aurora" (Au) as the pollen donor. A total of 49,826 SNPs were identified using the peach genome V2.1 as a reference. Then a stringent filtering was carried out, which revealed 1,441 high quality SNPs in 137 An x Au offspring, which were mapped in eight linkage groups. Finally, the consensus map was built using 732 SNPs which spanned 617 cM with an average of 0.96 cM between adjacent markers. The majority of the SNPs were distributed in the intragenic region in all the linkage groups. Considering all linkage groups together, 85.6% of the SNPs were located in intragenic regions and only 14.4% were located in intergenic regions. The genetic linkage analysis was able to co-localize two to three SNPs over 37 putative orthologous genes in eight linkage groups in the Japanese plum map. These results indicate a high level of synteny and collinearity between Japanese plum and peach genomes.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0208032PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277071PMC
May 2019

Nitrogen physiology of contrasting genotypes of Chenopodium quinoa Willd. (Amaranthaceae).

Sci Rep 2018 11 30;8(1):17524. Epub 2018 Nov 30.

Laboratorio de Genómica Funcional y Bioinformática, Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile.

Quinoa has been highlighted as a promising crop to sustain food security. The selection of physiological traits that allow identification genotypes with high Nitrogen use efficiency (NUE) is a key factor to increase Quinoa cultivation. In order to unveil the underpinning mechanisms for N-stress tolerance in Quinoa, three genotypes with similar phenology, but different NUE were developed under high (HN) or low (LN) nitrogen conditions. N metabolism processes and photosynthetic performance were studied after anthesis and in correlation with productivity to identify principal traits related to NUE. We found that protein content, net photosynthesis and leaf dry-mass were determinant attributes for yield at both HN and LN conditions. Contrastingly, the enhancement of N related metabolites ([Formula: see text], proline, betacyanins) and processes related with re-assimilation of [Formula: see text], including an increment of glutamine synthetase activity and up-regulation of CqAMT1,1 transporter expression in leaves, were negatively correlated with grain yield at both N conditions. Biochemical aspects of photosynthesis and root biomass were traits exclusively associated with grain yield at LN. The impact of N supply on seed quality is discussed. These results provide new insights towards the understanding the N metabolism of Quinoa.
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http://dx.doi.org/10.1038/s41598-018-34656-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6269519PMC
November 2018

Regeneration of highland papaya () from anther culture.

Appl Plant Sci 2018 Sep 24;6(9):e01182. Epub 2018 Sep 24.

Sociedad de Investigación y Servicios BioTECNOS Ltda. Camino a Pangal, Km 2.5 San Javier Chile.

Premise Of The Study: is an important Caricaceae species cultivated in several countries of South America. The objective of this study was to investigate different media compositions and plant growth regulators to induce plant regeneration.

Methods: Anthers were cultured in Murashige and Skoog medium with varying concentrations of naphthalene acetic acid (NAA) and 2,4-dichlorophenoxyacetic acid (2,4-D) plus a cytokinin (N-(2-chloro-4-pyridyl)-N'-phenylurea). The effect of the basal medium supplemented with auxins and cytokinins on shoot regeneration from the induced calli was also evaluated. Addition of maltose to the basal medium was also tested.

Results: The combination of 0.54 μM NAA and 22.66 μM 2,4-D induced the highest rate of calli formation. Regeneration via organogenesis was obtained in Murashige and Skoog and Woody Plant Medium supplemented with maltose and containing 8.88 μM 6-benzylaminopurine, 5.71 μM indoleacetic acid, and 2.28 μM zeatin.

Discussion: The plant regeneration protocol reported here permits the development of haploid and double haploid plants that can be useful for propagation purposes, allow a better molecular understanding of the species, and facilitate the production of new cultivars.
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http://dx.doi.org/10.1002/aps3.1182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6159643PMC
September 2018

Effect of sowing date and water availability on growth of plants of chia (Salvia hispanica L) established in Chile.

PLoS One 2018 12;13(9):e0203116. Epub 2018 Sep 12.

Laboratorio de Investigación en Ciencias Ambientales (LARES), Departamento de Ciencias Ambientales y Recursos Naturales Renovables, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile.

From 2010 to 2014 two trials were performed to assess the effect of sowing date (SD1, SD2) and irrigation treatments (IT1, IT2) on the growth of chia in central Chile, measuring leaf area (LA) and dry matter (DM) as primary parameters and relative growth rate (RGR), net assimilation rate (NAR), leaf weight ratio (LWR), crop growth rate (CGR) and specific leaf weight (SLW) as secondary parameters. Both LA and DM reached maximum values between 640 and 1150 accumulated degree days (ADD). However, LA and DM were 25% greater for sowing dates than for available water. Flowering date was also not affected by sowing date or water availability; plants flowered at 1140 and 942 ADD in SD1 and SD2 respectively, and at 499 ADD in the water availability trial. Sowing date had a significant effect on RGR 0.15 g g-1 d-1 for SD1 and 0.12 g g-1 d-1 for SD2 at 410 ADD. Greater water availability increased RGR by 60% compared to stressed plants, however NAR was similar between sowing dates with a tendency to greater values in SD2 plants; maximum values were recorded at 514 ADD in IT1 and IT2, with a tendency toward higher values in IT1. Thus, the primary growth variables LA, DM and flowering are genetically determined. However, the derived growth variables RGR, LWR, NAR, CGR and SLW were affected by sowing date and water availability, with significant differences at p≤ 0.05. The results showed that the sowing date and water availability influence significantly the growth parameters. The physiological component (NAR) show a strong influence on the growth rate of the chia (RGR), above the morphological component (SLW and LAR).
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203116PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135399PMC
February 2019

Evaluation of Morpho-Physiological Traits Adjustment of Under Long-Term Groundwater Depletion in the Hyper-Arid Atacama Desert.

Front Plant Sci 2018 9;9:453. Epub 2018 Apr 9.

Soil-Plant-Water Relations Laboratory, Agricultural Production Department, Faculty of Agronomical Sciences, Universidad de Chile, Santiago, Chile.

Water extraction from the underground aquifers of the Pampa del Tamarugal (Atacama Desert, Chile) reduced the growing area of , a strict phreatic species endemic to northern Chile. The objective of this work was to evaluate the effect of various architectural and morpho-physiological traits adjustment of subjected to three groundwater depletion intervals (GWDr): <1 m (control), 1-4 m and 6-9 m. The traits were evaluated at three levels, plant [height, trunk cross-section area, leaf fraction (GCC), and crown size], organ [length of internodes, leaf mass per unit area (LMA), leaflet mass and area], and tissue level [wood density (WD), leaf C, O isotope composition (δ), and intrinsic water use efficiency (iWUE)]. In addition, soil water content (VWC) to 1.3 m soil depth, pre-dawn and midday water potential difference (ΔΨ), and stomatal conductance (g) were evaluated. At the deeper GWDr, experienced significant growth restriction and reduced GCC, the remaining canopy had a significantly higher LMA associated with smaller leaflets. No differences in internode length and WD were observed. Values for δC and δO indicated that as GWDr increased, iWUE increased as a result of partial stomata closure with no significant effect on net assimilation over time. The morpho-physiological changes experienced by allowed it to acclimate and survive in a condition of groundwater depletion, keeping a functional but diminished canopy. These adjustments allowed maintenance of a relatively high g; ΔΨ was not different among GWDrs despite smaller VWC at greater GWDr. Although current conservation initiatives of this species are promising, forest deterioration is expected continue as groundwater depth increases.
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http://dx.doi.org/10.3389/fpls.2018.00453DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5900453PMC
April 2018

RNA-seq analysis of the head-kidney transcriptome response to handling-stress in the red cusk-eel (Genypterus chilensis).

Comp Biochem Physiol Part D Genomics Proteomics 2017 12 20;24:111-117. Epub 2017 Sep 20.

Universidad Andres Bello, Departamento Ciencias Biológicas, Facultad Ciencias Biológicas, 8370146 Santiago, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), 4030000 Concepción, Chile; Universidad Andres Bello, Centro de Investigación Marina Quintay (CIMARQ), Facultad de Ecología y Recursos Naturales, 2340000 Valparaíso, Chile. Electronic address:

Stress is a primary contributing factor of fish disease and mortality in aquaculture. We have previously reported that the red cusk-eel (Genypterus chilensis), an important farmed marine fish, demonstrates a handling-stress response that results in increased juvenile mortality, which is mainly associated with skeletal muscle atrophy and liver steatosis. To better understand the systemic effects of stress on red cusk-eel immune-related gene expression, the present study assessed the transcriptomic head-kidney response to handling-stress. The RNA sequencing generated a total of 61,655,525 paired-end reads from control and stressed conditions. De novo assembly using the CLC Genomic Workbench produced 86,840 transcripts and created a reference transcriptome with a N50 of 1426bp. Reads mapped onto the assembled reference transcriptome resulted in the identification of 569 up-regulated and 513 down-regulated transcripts. Gene ontology enrichment analysis revealed a significant up-regulation of the biological processes, like response to stress, response to biotic stimulus, and immune response. Conversely, a significant down-regulation of biological processes is associated with metabolic processes. These results were validated by RT-qPCR analysis for nine candidate genes involved in the immune response. The present data demonstrated that short term stress promotes the immune innate response in the marine teleost G. chilensis. This study is an important step towards understanding the immune adaptive response to stress in non-model teleost species.
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http://dx.doi.org/10.1016/j.cbd.2017.09.002DOI Listing
December 2017

Transcriptomic analysis of the hepatic response to stress in the red cusk-eel (Genypterus chilensis): Insights into lipid metabolism, oxidative stress and liver steatosis.

PLoS One 2017 27;12(4):e0176447. Epub 2017 Apr 27.

Universidad Andres Bello, Laboratorio de Biotecnología Molecular, Facultad Ciencias Biológicas, Santiago, Chile.

Teleosts exhibit a broad divergence in their adaptive response to stress, depending on the magnitude, duration, and frequency of stressors and the species receiving the stimulus. We have previously reported that the red cusk-eel (Genypterus chilensis), an important marine farmed fish, shows a physiological response to stress that results in increased skeletal muscle atrophy mediated by over-expression of components of the ubiquitin proteasome and autophagy-lysosomal systems. To better understand the systemic effects of stress on the red cusk-eel metabolism, the present study assessed the transcriptomic hepatic response to repetitive handling-stress. Using high-throughput RNA-seq, 259 up-regulated transcripts were found, mostly associated with angiogenesis, gluconeogenesis, and triacylglyceride catabolism. Conversely, 293 transcripts were down-regulated, associated to cholesterol biosynthesis, PPARα signaling, fatty acid biosynthesis, and glycolysis. This gene signature was concordant with hepatic metabolite levels and hepatic oxidative damage. Moreover, the increased plasmatic levels of AST (aspartate aminotransferase), ALT (alanine aminotransferase) and AP (alkaline phosphatase), as well as liver histology suggest stress-induced liver steatosis. This study offers an integrative molecular and biochemical analysis of the hepatic response to handling-stress, and reveals unknown aspects of lipid metabolism in a non-model teleost.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0176447PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5407771PMC
September 2017

Transcriptional Responses of Chilean Quinoa ( Willd.) Under Water Deficit Conditions Uncovers ABA-Independent Expression Patterns.

Front Plant Sci 2017 8;8:216. Epub 2017 Mar 8.

Laboratorio de Genómica Funcional & Bioinformática, Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Chile Santiago, Chile.

R49 genotype displayed best performance on selected physiological parameters and highest tolerance to drought.R49 drought over-represented transcripts has exhibited 19% of genes (306 contigs) that presented no homology to published databases.Expression pattern for canonical responses to drought such as ABA biosynthesis and other genes induced in response to drought were assessed by qPCR. Global freshwater shortage is one of the biggest challenges of our time, often associated to misuse, increased consumption demands and the effects of climate change, paralleled with the desertification of vast areas. (Willd.) represents a very promising species, due to both nutritional content and cultivation under water constraint. We characterized drought tolerance of three Chilean genotypes and selected Genotype R49 (Salares ecotype) based upon Relative Water Content (RWC), Electrolyte Leakage (EL) and maximum efficiency of photosystem II (F/F) after drought treatment, when compared to another two genotypes. Exploratory RNA-Seq of R49 was generated by Illumina paired-ends method comparing drought and control irrigation conditions. We obtained 104.8 million reads, with 54 million reads for control condition and 51 million reads for drought condition. Reads were assembled in 150,952 contigs, were 31,523 contigs have a reading frame of at least 300 nucleotides (100 aminoacids). BLAST2GO annotation showed a 15% of genes without homology to NCBI proteins, but increased to 19% (306 contigs) when focused into drought-induced genes. Expression pattern for canonical drought responses such as ABA biosynthesis and other genes induced were assessed by qPCR, suggesting novelty of R49 drought responses.
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http://dx.doi.org/10.3389/fpls.2017.00216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340777PMC
March 2017

De novo transcriptome assembly of 'Angeleno' and 'Lamoon' Japanese plum cultivars (Prunus salicina).

Genom Data 2016 Sep 19;9:35-6. Epub 2016 Jun 19.

Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Macul, Santiago, Chile.

Japanese plum (Prunus salicina L.) is a fruit tree of the Rosaceae family, which is an economically important stone fruit around the world. Currently, Japanese plum breeding programs combine traditional breeding and plant physiology strategies with genetic and genomic analysis. In order to understand the flavonoid pathway regulation and to develop molecular markers associated to the fuit skin color (EST-SSRs), we performed a next generation sequencing based on Illumina Hiseq2000 platform. A total of 22.4 GB and 21 GB raw data were obtained from 'Lamoon' and 'Angeleno' respectively, corresponding to 85,404,726 raw reads to 'Lamoon' and 79,781,666 to 'Angeleno'. A total of 139,775,975 reads were filtered after removing low-quality reads and trimming the adapter sequences. De novo transcriptome assembly was performed using CLC Genome Workbench software and a total of 54,584 unique contigs were generated, with an N50 of 1343 base pair (bp) and a mean length of 829 bp. This work contributed with a specific Japanese plum skin transcriptome, providing two libraries of contrasting fruit skin color phenotype (yellow and red) and increasing substantially the GB of raw data available until now for this specie.
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http://dx.doi.org/10.1016/j.gdata.2016.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4925449PMC
September 2016

Salares versus coastal ecotypes of quinoa: Salinity responses in Chilean landraces from contrasting habitats.

Plant Physiol Biochem 2016 Apr 22;101:1-13. Epub 2016 Jan 22.

Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Irnerio 42, 40126, Bologna, Italy.

Quinoa (Chenopodium quinoa Willd.) is a highly salt-tolerant species subdivided into five ecotypes and exhibiting broad intra-specific differences in tolerance levels. In a greenhouse study, Chilean landraces belonging either to the salares (R49) or coastal lowlands (VI-1, Villarrica) ecotype with contrasting agro-ecological origins were investigated for their responses to high salinity. The effects of two levels of salinity, 100 (T1) and 300 (T2) mM NaCl, on plant growth and on some physiological parameters were measured. Leaf and root Na(+) accumulation differed among landraces. T2 reduced growth and seed yield in all landraces with maximum inhibition relative to controls in R49. Salinity negatively affected chlorophyll and total polyphenol content (TPC) in VI-1 and Villarrica but not R49. Germination on saline or control media of seeds harvested from plants treated or not with NaCl was sometimes different; the best performing landrace was R49 insofar as 45-65% of seeds germinated on 500 mM NaCl-containing medium. In all landraces, average seedling root length declined strongly with increasing NaCl concentration, but roots of R49 were significantly longer than those of VI-1 and Villarrica up to 300 mM NaCl. Salt caused increases in seed TPC relative to controls, but radical scavenging capacity was higher only in seeds from T2 plants of R49. Total SDS-extractable seed proteins were resolved into distinct bands (10-70 kDa) with some evident differences between landraces. Salt-induced changes in protein patterns were landrace-specific. The responses to salinity of the salares landrace are discussed in relation to its better adaptation to an extreme environment.
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http://dx.doi.org/10.1016/j.plaphy.2016.01.010DOI Listing
April 2016

mRNA-seq reveals skeletal muscle atrophy in response to handling stress in a marine teleost, the red cusk-eel (Genypterus chilensis).

BMC Genomics 2015 Dec 1;16:1024. Epub 2015 Dec 1.

Laboratorio de Biotecnología Molecular, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile.

Background: Fish reared under intensive conditions are repeatedly exposed to stress, which negatively impacts growth. Although most fish follow a conserved pattern of stress response, with increased concentrations of cortisol, each species presents specificities in the cell response and stress tolerance. Therefore, culturing new species requires a detailed knowledge of these specific responses. The red cusk-eel (Genypterus chilensis) is a new economically important marine species for the Chilean aquaculture industry. However, there is no information on the stress- and cortisol-induced mechanisms that decrease skeletal muscle growth in this teleost.

Results: Using Illumina RNA-seq technology, skeletal muscle sequence reads for G. chilensis were generated under control and handling stress conditions. Reads were mapped onto a reference transcriptome, resulting in the in silico identification of 785 up-regulated and 167 down-regulated transcripts. Gene ontology enrichment analysis revealed a significant up-regulation of catabolic genes associated with skeletal muscle atrophy. These results were validated by RT-qPCR analysis for ten candidates genes involved in ubiquitin-mediated proteolysis, autophagy and skeletal muscle growth. Additionally, using a primary culture of fish skeletal muscle cells, the effect of cortisol was evaluated in relation to red cusk-eel skeletal muscle atrophy.

Conclusions: The present data demonstrated that handling stress promotes skeletal muscle atrophy in the marine teleost G. chilensis through the expression of components of the ubiquitin-proteasome and autophagy-lysosome systems. Furthermore, cortisol was a powerful inductor of skeletal muscle atrophy in fish myotubes. This study is an important step towards understanding the atrophy system in non-model teleost species and provides novel insights on the cellular and molecular mechanisms that control skeletal muscle growth in early vertebrates.
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http://dx.doi.org/10.1186/s12864-015-2232-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667402PMC
December 2015

Breeding in peach, cherry and plum: from a tissue culture, genetic, transcriptomic and genomic perspective.

Biol Res 2013 ;46(3):219-30

Laboratorio de Genómica Funcional & Bioinformática, Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile,

This review is an overview of traditional and modern breeding methodologies being used to develop new Prunus cultivars (stone fruits) with major emphasis on peach, sweet cherry and Japanese plum. To this end, common breeding tools used to produce seedlings, including in vitro culture tools, are discussed. Additionally, the mechanisms of inheritance of many important agronomical traits are described. Recent advances in stone fruit transcriptomics and genomic resources are providing an understanding of the molecular basis of phenotypic variability as well as the identification of allelic variants and molecular markers. These have potential applications for understanding the genetic diversity of the Prunus species, molecular marker-assisted selection and transgenesis. Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNPs) molecular markers are described as useful tools to describe genetic diversity in peach, sweet cherry and Japanese plum. Additionally, the recently sequenced peach genome and the public release of the sweet cherry genome are discussed in terms of their applicability to breeding programs.
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http://dx.doi.org/10.4067/S0716-97602013000300001DOI Listing
February 2016

Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica.

BMC Genomics 2013 Dec 16;14:885. Epub 2013 Dec 16.

Institute of Biotechnology and Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland.

Background: Through the diversity of cytokinin regulated processes, this phytohormone has a profound impact on plant growth and development. Cytokinin signaling is involved in the control of apical and lateral meristem activity, branching pattern of the shoot, and leaf senescence. These processes influence several traits, including the stem diameter, shoot architecture, and perennial life cycle, which define the development of woody plants. To facilitate research about the role of cytokinin in regulation of woody plant development, we have identified genes associated with cytokinin signaling and homeostasis pathways from two hardwood tree species.

Results: Taking advantage of the sequenced black cottonwood (Populus trichocarpa) and peach (Prunus persica) genomes, we have compiled a comprehensive list of genes involved in these pathways. We identified genes belonging to the six families of cytokinin oxidases (CKXs), isopentenyl transferases (IPTs), LONELY GUY genes (LOGs), two-component receptors, histidine containing phosphotransmitters (HPts), and response regulators (RRs). All together 85 Populus and 45 Prunus genes were identified, and compared to their Arabidopsis orthologs through phylogenetic analyses.

Conclusions: In general, when compared to Arabidopsis, differences in gene family structure were often seen in only one of the two tree species. However, one class of genes associated with cytokinin signal transduction, the CKI1-like family of two-component histidine kinases, was larger in both Populus and Prunus than in Arabidopsis.
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http://dx.doi.org/10.1186/1471-2164-14-885DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866579PMC
December 2013

Identification of volatile compounds associated with the aroma of white strawberries (Fragaria chiloensis).

J Sci Food Agric 2014 Mar 21;94(4):752-9. Epub 2013 Oct 21.

Universidad de Chile, Facultad de Ciencias Agronómicas, Departamento de Producción Agrícola, Laboratorio de Genómica Funcional & Bioinformática, 8820808, La Pintana, Santiago, Chile.

Background: Fragaria chiloensis (L.) Mill spp. chiloensis form chiloensis, is a strawberry that produces white fruits with unique aromas. This species, endemic to Chile, is one of the progenitors of Fragaria x ananassa Duch. In order to identify the volatile compounds that might be responsible for aroma, these were extracted, and analyzed by gas chromatography-mass spectrometry (GC-MS), gas chromatography-olfactometry (GC-O) and compared with sensory analyses.

Results: Three methods of extraction were used: solvent-assisted evaporation (SAFE), headspace solid phase micro-extraction (HS-SPME) and liquid-liquid extraction (LLE). Ninety-nine volatile compounds were identified by GC-MS, of which 75 showed odor activity using GC-O. Based on the highest dilution factor (FD = 1000) and GC-O intensity ≥2, we determined 20 major compounds in white strawberry fruit that contribute to its aroma. We chose 51 compounds to be tested against their commercial standards. The identities were confirmed by comparison of their linear retention indices against the commercial standards. The aroma of white strawberry fruits was reconstituted with a synthetic mixture of most of these compounds.

Conclusion: The volatile profile of white strawberry fruit described as fruity, green-fresh, floral, caramel, sweet, nutty and woody will be a useful reference for future strawberry breeding programs.
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http://dx.doi.org/10.1002/jsfa.6412DOI Listing
March 2014

Comparative genomics analysis in Prunoideae to identify biologically relevant polymorphisms.

Plant Biotechnol J 2013 Sep 13;11(7):883-93. Epub 2013 Jun 13.

Department of Horticulture, Washington State University, Pullman, WA, USA; Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, USA.

Prunus is an economically important genus with a wide range of physiological and biological variability. Using the peach genome as a reference, sequencing reads from four almond accessions and one sweet cherry cultivar were used for comparative analysis of these three Prunus species. Reference mapping enabled the identification of many biological relevant polymorphisms within the individuals. Examining the depth of the polymorphisms and the overall scaffold coverage, we identified many potentially interesting regions including hundreds of small scaffolds with no coverage from any individual. Non-sense mutations account for about 70 000 of the 13 million identified single nucleotide polymorphisms (SNPs). Blast2GO analyses on these non-sense SNPs revealed several interesting results. First, non-sense SNPs were not evenly distributed across all gene ontology terms. Specifically, in comparison with peach, sweet cherry is found to have non-sense SNPs in two 1-aminocyclopropane-1-carboxylate synthase (ACS) genes and two 1-aminocyclopropane-1-carboxylate oxidase (ACO) genes. These polymorphisms may be at the root of the nonclimacteric ripening of sweet cherry. A set of candidate genes associated with bitterness in almond were identified by comparing sweet and bitter almond sequences. To the best of our knowledge, this is the first report in plants of non-sense SNP abundance in a genus being linked to specific GO terms.
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http://dx.doi.org/10.1111/pbi.12081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3775899PMC
September 2013

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.

Nat Genet 2013 May 24;45(5):487-94. Epub 2013 Mar 24.

Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA)-Centro di Ricerca per la Frutticoltura, Rome, Italy.

Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.
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http://dx.doi.org/10.1038/ng.2586DOI Listing
May 2013

Construction and comparative analyses of highly dense linkage maps of two sweet cherry intra-specific progenies of commercial cultivars.

PLoS One 2013 31;8(1):e54743. Epub 2013 Jan 31.

Universidad Andrés Bello, Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Santiago, Chile.

Despite the agronomical importance and high synteny with other Prunus species, breeding improvements for cherry have been slow compared to other temperate fruits, such as apple or peach. However, the recent release of the peach genome v1.0 by the International Peach Genome Initiative and the sequencing of cherry accessions to identify Single Nucleotide Polymorphisms (SNPs) provide an excellent basis for the advancement of cherry genetic and genomic studies. The availability of dense genetic linkage maps in phenotyped segregating progenies would be a valuable tool for breeders and geneticists. Using two sweet cherry (Prunus avium L.) intra-specific progenies derived from crosses between 'Black Tartarian' × 'Kordia' (BT×K) and 'Regina' × 'Lapins'(R×L), high-density genetic maps of the four parental lines and the two segregating populations were constructed. For BT×K and R×L, 89 and 121 F(1) plants were used for linkage mapping, respectively. A total of 5,696 SNP markers were tested in each progeny. As a result of these analyses, 723 and 687 markers were mapped into eight linkage groups (LGs) in BT×K and R×L, respectively. The resulting maps spanned 752.9 and 639.9 cM with an average distance of 1.1 and 0.9 cM between adjacent markers in BT×K and R×L, respectively. The maps displayed high synteny and co-linearity between each other, with the Prunus bin map, and with the peach genome v1.0 for all eight LGs (LG1-LG8). These maps provide a useful tool for investigating traits of interest in sweet cherry and represent a qualitative advance in the understanding of the cherry genome and its synteny with other members of the Rosaceae family.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054743PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561380PMC
August 2013

The genome of woodland strawberry (Fragaria vesca).

Nat Genet 2011 Feb 26;43(2):109-16. Epub 2010 Dec 26.

Department of Biological Sciences, University of North Texas, Denton, Texas, USA.

The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.
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http://dx.doi.org/10.1038/ng.740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326587PMC
February 2011

Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE).

BMC Genomics 2010 Jan 18;11:43. Epub 2010 Jan 18.

Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile.

Background: Peach fruit undergoes a rapid softening process that involves a number of metabolic changes. Storing fruit at low temperatures has been widely used to extend its postharvest life. However, this leads to undesired changes, such as mealiness and browning, which affect the quality of the fruit. In this study, a 2-D DIGE approach was designed to screen for differentially accumulated proteins in peach fruit during normal softening as well as under conditions that led to fruit chilling injury.

Results: The analysis allowed us to identify 43 spots -representing about 18% of the total number analyzed- that show statistically significant changes. Thirty-nine of the proteins could be identified by mass spectrometry. Some of the proteins that changed during postharvest had been related to peach fruit ripening and cold stress in the past. However, we identified other proteins that had not been linked to these processes. A graphical display of the relationship between the differentially accumulated proteins was obtained using pairwise average-linkage cluster analysis and principal component analysis. Proteins such as endopolygalacturonase, catalase, NADP-dependent isocitrate dehydrogenase, pectin methylesterase and dehydrins were found to be very important for distinguishing between healthy and chill injured fruit. A categorization of the differentially accumulated proteins was performed using Gene Ontology annotation. The results showed that the 'response to stress', 'cellular homeostasis', 'metabolism of carbohydrates' and 'amino acid metabolism' biological processes were affected the most during the postharvest.

Conclusions: Using a comparative proteomic approach with 2-D DIGE allowed us to identify proteins that showed stage-specific changes in their accumulation pattern. Several proteins that are related to response to stress, cellular homeostasis, cellular component organization and carbohydrate metabolism were detected as being differentially accumulated. Finally, a significant proportion of the proteins identified had not been associated with softening, cold storage or chilling injury-altered fruit before; thus, comparative proteomics has proven to be a valuable tool for understanding fruit softening and postharvest.
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http://dx.doi.org/10.1186/1471-2164-11-43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2822761PMC
January 2010

Isolation and functional characterization of cold-regulated promoters, by digitally identifying peach fruit cold-induced genes from a large EST dataset.

BMC Plant Biol 2009 Sep 22;9:121. Epub 2009 Sep 22.

Millennium Nucleus in Plant Cell Biotechnology (MN-PCB), Santiago, Chile.

Background: Cold acclimation is the process by which plants adapt to the low, non freezing temperatures that naturally occur during late autumn or early winter. This process enables the plants to resist the freezing temperatures of winter. Temperatures similar to those associated with cold acclimation are also used by the fruit industry to delay fruit ripening in peaches. However, peaches that are subjected to long periods of cold storage may develop chilling injury symptoms (woolliness and internal breakdown). In order to better understand the relationship between cold acclimation and chilling injury in peaches, we isolated and functionally characterized cold-regulated promoters from cold-inducible genes identified by digitally analyzing a large EST dataset.

Results: Digital expression analyses of EST datasets, revealed 164 cold-induced peach genes, several of which show similarities to genes associated with cold acclimation and cold stress responses. The promoters of three of these cold-inducible genes (Ppbec1, Ppxero2 and Pptha1) were fused to the GUS reporter gene and characterized for cold-inducibility using both transient transformation assays in peach fruits (in fruta) and stable transformation in Arabidopsis thaliana. These assays demonstrate that the promoter Pptha1 is not cold-inducible, whereas the Ppbec1 and Ppxero2 promoter constructs are cold-inducible.

Conclusion: This work demonstrates that during cold storage, peach fruits differentially express genes that are associated with cold acclimation. Functional characterization of these promoters in transient transformation assays in fruta as well as stable transformation in Arabidopsis, demonstrate that the isolated Ppbec1 and Ppxero2 promoters are cold-inducible promoters, whereas the isolated Pptha1 promoter is not cold-inducible. Additionally, the cold-inducible activity of the Ppbec1 and Ppxero2 promoters suggest that there is a conserved heterologous cold-inducible regulation of these promoters in peach and Arabidopsis. These results reveal that digital expression analyses may be used in non-model species to identify candidate genes whose promoters are differentially expressed in response to exogenous stimuli.
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http://dx.doi.org/10.1186/1471-2229-9-121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754992PMC
September 2009

Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality.

BMC Genomics 2009 Sep 10;10:423. Epub 2009 Sep 10.

Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile.

Background: Cold storage is used to inhibit peach fruit ripening during shipment to distant markets. However, this cold storage can negatively affect the quality of the fruit when it is ripened, resulting in disorders such as wooliness, browning or leathering. In order to understand the individual and combined biological effects that factors such as cold storage and ripening have on the fruit and fruit quality, we have taken a comparative EST transcript profiling approach to identify genes that are differentially expressed in response to these factors.

Results: We sequenced 50,625 Expressed Sequence Tags (ESTs) from peach mesocarp (Prunus persica O'Henry variety) stored at four different postharvest conditions. A total of 10,830 Unigenes (4,169 contigs and 6,661 singletons) were formed by assembling these ESTs. Additionally, a collection of 614 full-length and 1,109 putative full-length cDNA clones within flanking loxP recombination sites was created. Statistically analyzing the EST population, we have identified genes that are differentially expressed during ripening, in response to cold storage or the combined effects of cold storage and ripening. Pair-wise comparisons revealed 197 contigs with at least one significant difference in transcript abundance between at least two conditions. Gene expression profile analyses revealed that the contigs may be classified into 13 different clusters of gene expression patterns. These clusters include groups of contigs that increase or decrease transcript abundance during ripening, in response to cold or ripening plus cold.

Conclusion: These analyses have enabled us to statistically identify novel genes and gene clusters that are differentially expressed in response to post-harvest factors such as long-term cold storage, ripening or a combination of these two factors. These differentially expressed genes reveal the complex biological processes that are associated with these factors, as well as a large number of putative gene families that may participate differentially in these processes. In particular, these analyzes suggest that woolly fruits lack the increased boost of metabolic processes necessary for ripening. Additionally, these results suggest that the mitochondria and plastids play a major role in these processes. The EST sequences and full-length cDNA clones developed in this work, combined with the large population of differentially expressed genes may serve as useful tools and markers that will enable the scientific community to better define the molecular processes that affect fruit quality in response to post-harvest conditions and the organelles that participate in these processes.
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http://dx.doi.org/10.1186/1471-2164-10-423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748099PMC
September 2009

Identification of woolliness response genes in peach fruit after post-harvest treatments.

J Exp Bot 2008 3;59(8):1973-86. Epub 2008 May 3.

Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, Millennium Nucleus Center for Genomics of the Cell (CGC), Santiago, Chile.

Woolliness is a physiological disorder of peaches and nectarines that becomes apparent when fruit are ripened after prolonged periods of cold storage. This disorder is of commercial importance since shipping of peaches to distant markets and storage before selling require low temperature. However, knowledge about the molecular basis of peach woolliness is still incomplete. To address this issue, a nylon macroarray containing 847 non-redundant expressed sequence tags (ESTs) from a ripe peach fruit cDNA library was developed and used. Gene expression changes of peach fruit (Prunus persica cv. O'Henry) ripened for 7 d at 21 degrees C (juicy fruit) were compared with those of fruit stored for 15 d at 4 degrees C and then ripened for 7 d at 21 degrees C (woolly fruit). A total of 106 genes were found to be differentially expressed between juicy and woolly fruit. Data analysis indicated that the activity of most of these genes (>90%) was repressed in the woolly fruit. In cold-stored peaches (cv. O'Henry), the expression level of selected genes (cobra, endopolygalacturonase, cinnamoyl-CoA-reductase, and rab11) was lower than in the juicy fruit, and it remained low in woolly peaches after ripening, a pattern that was conserved in woolly fruit from two other commercial cultivars (cv. Flamekist and cv. Elegant Lady). In addition, the results of this study indicate that molecular changes during fruit woolliness involve changes in the expression of genes associated with cell wall metabolism and endomembrane trafficking. Overall, the results reported here provide an initial characterization of the transcriptome activity of peach fruit under different post-harvest treatments.
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http://dx.doi.org/10.1093/jxb/ern069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2413281PMC
July 2008

Relationship between grain yield, osmotic adjustment and benzoxazinone content in Triticum aestivum L. cultivars.

Z Naturforsch C J Biosci 2006 Sep-Oct;61(9-10):704-8

Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile.

Fifteen wheat genotypes were grown under water deficit to ascertain the role of osmotic adjustment (OA) and the concentration of benzoxazinones in sustaining grain yield. A positive correlation between osmotic adjustment capacity and yield was observed in wheat genotypes cultivated under field conditions. The weight gain of plants exposed to drought was in agreement with the OA values (R(2) = 0.93). However, when wheat plants were infested by cereal aphids, this correlation was not found. The benzoxazinones 2,4-dihydroxy-1,4-benzoxa-zin-3-one (DIBOA) and 2,4-dihydroxy-7-methoxy-1,4 benzoxazin-3-one (DIMBOA) are defensive secondary metabolites present in wheat and others cereals. The content of these compounds varied in wheat genotypes and increased with drought and aphid infestation. A positive correlation between weight gain of irrigated-infested plants and drought-infested plants and the contents of benzoxazinones was observed. These results suggest that plants with better OA capacity and high benzoxazinone content should have better field yields.
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http://dx.doi.org/10.1515/znc-2006-9-1016DOI Listing
January 2007

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

BMC Bioinformatics 2006 Nov 23;7:513. Epub 2006 Nov 23.

Millennium Nucleus in Plant Cell Biology and Plant Biotechnology Center, Andres Bello University, Santiago, Chile.

Background: Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task.

Results: In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access.

Conclusion: JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from http://genoma.unab.cl/juice_system/ or http://www.genomavegetal.cl/juice_system/.
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http://dx.doi.org/10.1186/1471-2105-7-513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1676024PMC
November 2006

The Ca2+ pump inhibitor, thapsigargin, inhibits root gravitropism in Arabidopsis thaliana.

Biol Res 2006 25;39(2):289-96. Epub 2006 Jul 25.

Millennium Nucleus in Plant Cell Biology and Centro de Biotecnología Vegetal, Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Santiago, Chile.

Thapsigargin, a specific inhibitor of most animal intracellular SERCA-type Ca2+ pumps present in the sarcoplasmic/endoplasmic reticulum, was originally isolated from the roots of the Mediterranean plant Thapsia gargancia L. Here, we demonstrate that this root-derived compound is capable of altering root gravitropism in Arabidopsis thaliana. Thapsigargin concentrations as low as 0.1 microM alter root gravitropism whereas under similar conditions cyclopiazonic acid does not. Furthermore, a fluorescently conjugated thapsigargin (BODIPY FL thapsigargin) suggests that target sites for thapsigargin are located in intracellular organelles in the root distal elongation zone and the root cap, regions known to regulate root gravitropism.
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http://dx.doi.org/10.4067/s0716-97602006000200011DOI Listing
March 2007

Arabidopsis thaliana: a model host plant to study plant-pathogen interaction using Chilean field isolates of Botrytis cinerea.

Biol Res 2006 25;39(2):221-8. Epub 2006 Jul 25.

Laboratorio de Genética Molecular Vegetal, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.

One of the fungal pathogens that causes more agriculture damage is Botrytis cinerea. Botrytis is a constant threat to crops because the fungus infects a wide range of host species, both native and cultivated. Furthermore, Botrytis persists on plant debris in and on the soil. Some of the most serious diseases caused by Botrytis include gray mold on vegetables and fruits, such as grapes and strawberries. Botrytis also causes secondary soft rot of fruits and vegetables during storage, transit and at the market. In many plant-pathogen interactions, resistance often is associated with the deposition of callose, accumulation of autofluorescent compounds, the synthesis and accumulation of salicylic acid as well as pathogenesis-related proteins. Arabidopsis thaliana has been used as a plant model to study plant-pathogen interaction. The genome of Arabidopsis has been completely sequenced and this plant serves as a good genetic and molecular model. In this study, we demonstrate that Chilean field isolates infect Arabidopsis thaliana and that Arabidopsis subsequently activates several defense response mechanisms associated with a hypersensitive response. Furthermore, we propose that Arabidopsis may be used as a model host species to analyze the diversity associated with infectivity among populations of Botrytis cinerea field isolates.
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http://dx.doi.org/10.4067/s0716-97602006000200004DOI Listing
March 2007

AtUTr1, a UDP-glucose/UDP-galactose transporter from Arabidopsis thaliana, is located in the endoplasmic reticulum and up-regulated by the unfolded protein response.

J Biol Chem 2006 Apr 8;281(14):9145-51. Epub 2006 Feb 8.

Plant Cell Biology Millennium Nucleus, Graduate School, Faculty of Sciences, University of Chile, Casilla 653, Santiago, Chile.

The folding of glycoproteins in the endoplasmic reticulum (ER) depends on a quality control mechanism mediated by the calnexin/calreticulin cycle. During this process, continuous glucose trimming and UDP-glucose-dependent re-glucosylation of unfolded glycoproteins takes place. To ensure proper folding, increases in misfolded proteins lead to up-regulation of the components involved in quality control through a process known as the unfolded protein response (UPR). Reglucosylation is catalyzed by the ER lumenal located enzyme UDP-glucose glycoprotein glucosyltransferase, but as UDP-glucose is synthesized in the cytosol, a UDP-glucose transporter is required in the calnexin/calreticulin cycle. Even though such a transporter has been hypothesized, no protein playing this role in the ER yet has been identified. Here we provide evidence that AtUTr1, a UDP-galactose/glucose transporter from Arabidopsis thaliana, responds to stimuli that trigger the UPR increasing its expression around 9-fold. The accumulation of AtUTr1 transcript is accompanied by an increase in the level of the AtUTr1 protein. Moreover, subcellular localization studies indicate that AtUTr1 is localized in the ER of plant cells. We reasoned that an impairment in AtUTr1 expression should perturb the calnexin/calreticulin cycle leading to an increase in misfolded protein and triggering the UPR. Toward that end, we analyzed an AtUTr1 insertional mutant and found an up-regulation of the ER chaperones BiP and calnexin, suggesting that these plants may be constitutively activating the UPR. Thus, we propose that in A. thaliana, AtUTr1 is the UDP-glucose transporter involved in quality control in the ER.
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http://dx.doi.org/10.1074/jbc.M512210200DOI Listing
April 2006
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