Publications by authors named "Ariel Orellana"

53 Publications

Transport of UDP-rhamnose by URGT2, URGT4, and URGT6 modulates rhamnogalacturonan-I length.

Plant Physiol 2021 Apr;185(3):914-933

Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago 8370146, Chile.

Rhamnogalacturonan-I biosynthesis occurs in the lumen of the Golgi apparatus, a compartment where UDP-Rhamnose and UDP-Galacturonic Acid are the main substrates for synthesis of the backbone polymer of pectin. Recent studies showed that UDP-Rha is transported from the cytosol into the Golgi apparatus by a family of six UDP-rhamnose/UDP-galactose transporters (URGT1-6). In this study, analysis of adherent and soluble mucilage (SM) of Arabidopsis thaliana seeds revealed distinct roles of URGT2, URGT4, and URGT6 in mucilage biosynthesis. Characterization of SM polymer size showed shorter chains in the urgt2 urgt4 and urgt2 urgt4 urgt6 mutants, suggesting that URGT2 and URGT4 are mainly involved in Rhamnogalacturonan-I (RG-I) elongation. Meanwhile, mutants in urgt6 exhibited changes only in adherent mucilage (AM). Surprisingly, the estimated number of RG-I polymer chains present in urgt2 urgt4 and urgt2 urgt4 urgt6 mutants was higher than in wild-type. Interestingly, the increased number of shorter RG-I chains was accompanied by an increased amount of xylan. In the urgt mutants, expression analysis of other genes involved in mucilage biosynthesis showed some compensation. Studies of mutants of transcription factors regulating mucilage formation indicated that URGT2, URGT4, and URGT6 are likely part of a gene network controlled by these regulators and involved in RG-I synthesis. These results suggest that URGT2, URGT4, and URGT6 play different roles in the biosynthesis of mucilage, and the lack of all three affects the production of shorter RG-I polymers and longer xylan domains.
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http://dx.doi.org/10.1093/plphys/kiaa070DOI Listing
April 2021

SARS-CoV-2 infection in asymptomatic healthcare workers at a clinic in Chile.

PLoS One 2021 28;16(1):e0245913. Epub 2021 Jan 28.

Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.

Asymptomatic SARS-CoV-2 infection of healthcare workers (HCWs) has been reported as a key player in the nosocomial spreading of COVID-19. Early detection of infected HCWs can prevent spreading of the virus in hospitals among HCWs and patients. We conducted a cross-sectional study to determine the asymptomatic infection of HCWs in a private clinic in the city of Santiago, Chile. Our study was conducted during a period of 5 weeks at the peak of transmission of SARS-CoV-2 in Chile. Nasopharyngeal samples were obtained from 413 HCWs and tested for the presence of SARS-CoV-2 using RT-qPCR. We found that a 3.14% of HCWs were positive for the presence of SARS-CoV-2 (14/413). Out of these, 7/14 were completely asymptomatic and did not develop symptoms within 3 weeks of testing. Sequencing of viral genomes showed the predominance of the GR clade; however, sequence comparison demonstrated numerous genetic differences among them suggesting community infection as the main focus of transmission among HCWs. Our study demonstrates that the protocols applied to protect HCWs and patients have been effective as no infection clusters due to asymptomatic carriers were found in the clinic. Together, these data suggest that infection with SARS-CoV-2 among HCWs of this health center is not nosocomial.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245913PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7842995PMC
February 2021

Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening.

BMC Genomics 2021 Jan 6;22(1):17. Epub 2021 Jan 6.

Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide, 5750, Huechuraba, Chile.

Background: Fruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening.

Results: To accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O'Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2740 proteins, using the peach genome reference v1. After data pre-treatment, 1663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase, a homeobox-leucine zipper protein and an ACC oxidase. Transcription factors enriched in NAC and Myb protein domains would target preferentially the genes encoding proteins more abundant in mature and ripe fruit, respectively.

Conclusions: Shotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from mature to ripe fruit.
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http://dx.doi.org/10.1186/s12864-020-07299-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7788829PMC
January 2021

Functional Interchangeability of Nucleotide Sugar Transporters URGT1 and URGT2 Reveals That and Cell Wall Chemotypes Depend on Their Spatio-Temporal Expression.

Front Plant Sci 2020 8;11:594544. Epub 2020 Dec 8.

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

Nucleotide sugar transporters (NSTs) are Golgi-localized proteins that play a role in polysaccharide biosynthesis by transporting substrates (nucleotide sugars) from the cytosol into the Golgi apparatus. In Arabidopsis, there is an NST subfamily of six members, called URGTs, which transport UDP-rhamnose and UDP-galactose . URGTs are very similar in protein sequences, and among them, URGT1 and URGT2 are highly conserved in protein sequence and also showed very similar kinetic parameters toward UDP-rhamnose and UDP-galactose . Despite the similarity in sequence and function, mutants in led to a specific reduction in galactose in rosette leaves. In contrast, mutants in showed a decrease in rhamnose content in soluble mucilage from seeds. Given these specific and quite different chemotypes, we wonder whether the differences in gene expression could explain the observed differences between the mutants. Toward that end, we analyzed whether URGT2 could rescue the phenotype and by performing a promoter swapping experiment. We analyzed whether the expression of the coding sequence, controlled by the promoter, could rescue the rosette phenotype. A similar strategy was used to determine whether URGT1 could rescue the mucilage phenotype. Expression analysis of the swapped genes, using qRT-PCR, was similar to the native and genes in wild-type plants. To monitor the protein expression of the swapped genes, both URGTs were tagged with green fluorescent protein (GFP). Confocal microscopy analyses of the swapped lines containing URGT2-GFP showed fluorescence in motile dot-like structures in rosette leaves. Swapped lines containing URGT1-GFP showed fluorescence in dot-like structures in the seed coat. Finally, the expression of in mutants rescued galactose reduction in rosette leaves. In the same manner, the expression of in mutants recovered the content of rhamnose in soluble mucilage. Hence, our results showed that their expression in different organs modulates the role of URGT1 and URGT2. Likely, this is due to their presence in different cellular contexts, where other proteins, acting in partnership, may drive their functions toward different pathways.
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http://dx.doi.org/10.3389/fpls.2020.594544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7752924PMC
December 2020

Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches.

BMC Plant Biol 2020 Aug 3;20(1):365. Epub 2020 Aug 3.

Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile.

Background: Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. However, berry size is a complex quantitive trait under polygenic control, and its genetic determination of berry weight is not yet fully understood. The aim of this work was to perform marker discovery using a transcriptomic approach, in order to identify and characterize SNP and InDel markers associated with berry size in table grapes. We used an integrative analysis based on RNA-Seq, SNP/InDel search and validation on table grape segregants and varieties with different genetic backgrounds.

Results: Thirty SNPs and eight InDels were identified using a transcriptomic approach (RNA-Seq). These markers were selected from SNP/InDel found among segregants from a Ruby x Sultanina population with contrasting phenotypes for berry size. The set of 38 SNP and InDel markers was distributed in eight chromosomes. Genotype-phenotype association analyses were performed using a set of 13 RxS segregants and 41 table grapes varieties with different genetic backgrounds during three seasons. The results showed several degrees of association of these markers with berry size (10.2 to 30.7%) as other berry-related traits such as length and width. The co-localization of SNP and /or InDel markers and previously reported QTLs and candidate genes associated with berry size were analysed.

Conclusions: We identified a set of informative and transferable SNP and InDel markers associated with berry size. Our results suggest the suitability of SNPs and InDels as candidate markers for berry weight in seedless table grape breeding. The identification of genomic regions associated with berry weight in chromosomes 8, 15 and 17 was achieved with supporting evidence derived from a transcriptome experiment focused on SNP/InDel search, as well as from a QTL-linkage mapping approach. New regions possibly associated with berry weight in chromosomes 3, 6, 9 and 14 were identified.
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http://dx.doi.org/10.1186/s12870-020-02564-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397606PMC
August 2020

New steps in mucilage biosynthesis revealed by analysis of the transcriptome of the UDP-rhamnose/UDP-galactose transporter 2 mutant.

J Exp Bot 2019 10;70(19):5071-5088

Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.

Upon imbibition, epidermal cells of Arabidopsis thaliana seeds release a mucilage formed mostly by pectic polysaccharides. The Arabidopsis mucilage is composed mainly of unbranched rhamnogalacturonan-I (RG-I), with low amounts of cellulose, homogalacturonan, and traces of xylan, xyloglucan, galactoglucomannan, and galactan. The pectin-rich composition of the mucilage and their simple extractability makes this structure a good candidate to study the biosynthesis of pectic polysaccharides and their modification. Here, we characterize the mucilage phenotype of a mutant in the UDP-rhamnose/galactose transporter 2 (URGT2), which exhibits a reduction in RG-I and also shows pleiotropic changes, suggesting the existence of compensation mechanisms triggered by the lack of URGT2. To gain an insight into the possible compensation mechanisms activated in the mutant, we performed a transcriptome analysis of developing seeds using RNA sequencing (RNA-seq). The results showed a significant misregulation of 3149 genes, 37 of them (out of the 75 genes described to date) encoding genes proposed to be involved in mucilage biosynthesis and/or its modification. The changes observed in urgt2 included the up-regulation of UAFT2, a UDP-arabinofuranose transporter, and UUAT3, a paralog of the UDP-uronic acid transporter UUAT1, suggesting that they play a role in mucilage biosynthesis. Mutants in both genes showed changes in mucilage composition and structure, confirming their participation in mucilage biosynthesis. Our results suggest that plants lacking a UDP-rhamnose/galactose transporter undergo important changes in gene expression, probably to compensate modifications in the plant cell wall due to the lack of a gene involved in its biosynthesis.
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http://dx.doi.org/10.1093/jxb/erz262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6793455PMC
October 2019

Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans.

Sci Rep 2019 02 14;9(1):2132. Epub 2019 Feb 14.

FONDAP Center for Genome Regulation, Santiago, Chile.

Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native Americans, especially those from the Southern Cone is scant. Here we present annotation and variant discovery from high-quality complete genome sequences of a cohort of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately 3.1 × 10 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs events. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a sample from a marginally admixed population from the Southern Cone, whose main genetic component derives from Native American ancestors. Additionally, we found that HUI genomes contain variants in genes associated with 5 of the 6 leading causes of noncommunicable diseases in Chile, which may have an impact on the risk of prevalent diseases in Chilean and Amerindian populations. Our data represents a useful resource that can contribute to population-based studies and for the design of early diagnostics or prevention tools for Native and admixed Latin American populations.
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http://dx.doi.org/10.1038/s41598-019-39391-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376018PMC
February 2019

Comparative Transcriptome Profiling in a Segregating Peach Population with Contrasting Juiciness Phenotypes.

J Agric Food Chem 2019 Feb 24;67(5):1598-1607. Epub 2019 Jan 24.

Laboratorio de Bioinformática y Expresión Génica , Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile , Av. El Líbano 5524 , Santiago , Chile.

Cold storage of fruit is one of the methods most commonly employed to extend the postharvest lifespan of peaches ( Prunus persica (L.) Batsch). However, fruit quality in this species is affected negatively by mealiness, a physiological disorder triggered by chilling injury after long periods of exposure to low temperatures during storage and manifested mainly as a lack of juiciness, which ultimately modifies the organoleptic properties of peach fruit. The aim of this study was to identify molecular components and metabolic processes underlying mealiness in susceptible and nonsusceptible segregants. Transcriptome and qRT-PCR profiling were applied to individuals with contrasting juiciness phenotypes in a segregating F population. Our results suggest that mealiness is a multiscale phenomenon, because juicy and mealy fruit display distinctive reprogramming processes affecting translational machinery and lipid, sugar, and oxidative metabolism. The candidate genes identified may be useful tools for further crop improvement.
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http://dx.doi.org/10.1021/acs.jafc.8b05177DOI Listing
February 2019

A Prunus persica genome-wide RNA-seq approach uncovers major differences in the transcriptome among chilling injury sensitive and non-sensitive varieties.

Physiol Plant 2019 Jul 21;166(3):772-793. Epub 2018 Oct 21.

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

Chilling injury represents a major constrain for crops productivity. Prunus persica, one of the most relevant rosacea crops, have early season varieties that are resistant to chilling injury, in contrast to late season varieties, which display chilling symptoms such as mealiness (dry, sandy fruit mesocarp) after prolonged storage at chilling temperatures. To uncover the molecular processes related to the ability of early varieties to withstand mealiness, postharvest and genome-wide RNA-seq assessments were performed in two early and two late varieties. Differences in juice content and ethylene biosynthesis were detected among early and late season fruits that became mealy after exposed to prolonged chilling. Principal component and data distribution analysis revealed that cold-stored late variety fruit displayed an exacerbated and unique transcriptome profile when compared to any other postharvest condition. A differential expression analysis performed using an empirical Bayes mixture modeling approach followed by co-expression and functional enrichment analysis uncover processes related to ethylene, lipids, cell wall, carotenoids and DNA metabolism, light response, and plastid homeostasis associated to the susceptibility or resistance of P. persica varieties to chilling stress. Several of the genes related to these processes are in quantitative trait loci (QTL) associated to mealiness in P. persica. Together, these analyses exemplify how P. persica can be used as a model for studying chilling stress in plants.
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http://dx.doi.org/10.1111/ppl.12831DOI Listing
July 2019

bZIP17 regulates the expression of genes related to seed storage and germination, reducing seed susceptibility to osmotic stress.

J Cell Biochem 2018 08 25;119(8):6857-6868. Epub 2018 Apr 25.

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

Low temperatures, salinity, and drought cause significant crop losses. These conditions involve osmotic stress, triggering transcriptional remodeling, and consequently, the restitution of cellular homeostasis and growth recovery. Protein transcription factors regulate target genes, thereby mediating plant responses to stress. bZIP17 is a transcription factor involved in cellular responses to salinity and the unfolded protein response. Because salinity can also produce osmotic stress, the role of bZIP17 in response to osmotic stress was assessed. Mannitol treatments induced the transcript accumulation and protein processing of bZIP17. Transcriptomic analyses showed that several genes associated with seed storage and germination showed lower expression in bzip17 mutants than in wild-type plants. Interestingly, bZIP17 transcript was more abundant in seeds, and germination analyses revealed that wild-type plants germinated later than bzip17 mutants in the presence of mannitol, but no effects were observed when the seeds were exposed to ABA. Finally, the transcript levels of bZIP17 target genes that control seed storage and germination were assessed in seeds exposed to mannitol treatments, which showed lower expression levels in bzip17 mutants compared to the wild-type seeds. These results suggest that bZIP17 plays a role in osmotic stress, acting as a negative regulator of germination through the regulation of genes involved in seed storage and germination.
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http://dx.doi.org/10.1002/jcb.26882DOI Listing
August 2018

Global gene expression analysis provides insight into local adaptation to geothermal streams in tadpoles of the Andean toad Rhinella spinulosa.

Sci Rep 2017 05 16;7(1):1966. Epub 2017 May 16.

Center for Genome Regulation, Blanco Encalada 2085, Santiago, Chile.

The anuran Rhinella spinulosa is distributed along the Andes Range at altitudes that undergo wide daily and seasonal variation in temperature. One of the populations inhabits geothermal streams, a stable environment that influences life history traits such as the timing of metamorphosis. To investigate whether this population has undergone local adaptation to this unique habitat, we carried out transcriptome analyses in animals from two localities in two developmental stages (prometamorphic and metamorphic) and exposed them to two temperatures (20 and 25 °C). RNA-Seq, de novo assembly and annotation defined a transcriptome revealing 194,469 high quality SNPs, with 1,507 genes under positive selection. Comparisons among the experimental conditions yielded 1,593 differentially expressed genes. A bioinformatics search for candidates revealed a total of 70 genes that are highly likely to be implicated in the adaptive response of the population living in a stable environment, compared to those living in an environment with variable temperatures. Most importantly, the population inhabiting the geothermal environment showed decreased transcriptional plasticity and reduced genetic variation compared to its counterpart from the non-stable environment. This analysis will help to advance the understanding of the molecular mechanisms that account for the local adaptation to geothermal streams in anurans.
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http://dx.doi.org/10.1038/s41598-017-01982-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5434060PMC
May 2017

The elaborate route for UDP-arabinose delivery into the Golgi of plants.

Proc Natl Acad Sci U S A 2017 04 3;114(16):4261-4266. Epub 2017 Apr 3.

School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia;

In plants, L-arabinose (Ara) is a key component of cell wall polymers, glycoproteins, as well as flavonoids, and signaling peptides. Whereas the majority of Ara found in plant glycans occurs as a furanose ring (Ara), the activated precursor has a pyranose ring configuration (UDP-Ara). The biosynthesis of UDP-Ara mainly occurs via the epimerization of UDP-xylose (UDP-Xyl) in the Golgi lumen. Given that the predominant Ara form found in plants is Ara, UDP-Ara must exit the Golgi to be interconverted into UDP-Ara by UDP-Ara mutases that are located outside on the cytosolic surface of the Golgi. Subsequently, UDP-Ara must be transported back into the lumen. This step is vital because glycosyltransferases, the enzymes mediating the glycosylation reactions, are located within the Golgi lumen, and UDP-Ara, synthesized within the Golgi, is not their preferred substrate. Thus, the transport of UDP-Ara into the Golgi is a prerequisite. Although this step is critical for cell wall biosynthesis and the glycosylation of proteins and signaling peptides, the identification of these transporters has remained elusive. In this study, we present data demonstrating the identification and characterization of a family of Golgi-localized UDP-Ara transporters in The application of a proteoliposome-based transport assay revealed that four members of the nucleotide sugar transporter (NST) family can efficiently transport UDP-Ara in vitro. Subsequent analysis of mutant lines affected in the function of these NSTs confirmed their role as UDP-Ara transporters in vivo.
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http://dx.doi.org/10.1073/pnas.1701894114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5402404PMC
April 2017

UUAT1 Is a Golgi-Localized UDP-Uronic Acid Transporter That Modulates the Polysaccharide Composition of Arabidopsis Seed Mucilage.

Plant Cell 2017 01 6;29(1):129-143. Epub 2017 Jan 6.

Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile

UDP-glucuronic acid (UDP-GlcA) is the precursor of many plant cell wall polysaccharides and is required for production of seed mucilage. Following synthesis in the cytosol, it is transported into the lumen of the Golgi apparatus, where it is converted to UDP-galacturonic acid (UDP-GalA), UDP-arabinose, and UDP-xylose. To identify the Golgi-localized UDP-GlcA transporter, we screened mutants in genes coding for putative nucleotide sugar transporters for altered seed mucilage, a structure rich in the GalA-containing polysaccharide rhamnogalacturonan I. As a result, we identified , which encodes a Golgi-localized protein that transports UDP-GlcA and UDP-GalA in vitro. The seed coat of mutants had less GalA, rhamnose, and xylose in the soluble mucilage, and the distal cell walls had decreased arabinan content. Cell walls of other organs and cells had lower arabinose levels in roots and pollen tubes, but no differences were observed in GalA or xylose contents. Furthermore, the GlcA content of glucuronoxylan in the stem was not affected in the mutant. Interestingly, the degree of homogalacturonan methylation increased in These results suggest that this UDP-GlcA transporter plays a key role defining the seed mucilage sugar composition and that its absence produces pleiotropic effects in this component of the plant extracellular matrix.
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http://dx.doi.org/10.1105/tpc.16.00465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5304346PMC
January 2017

The Root Hair Specific SYP123 Regulates the Localization of Cell Wall Components and Contributes to Rizhobacterial Priming of Induced Systemic Resistance.

Front Plant Sci 2016 26;7:1081. Epub 2016 Jul 26.

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

Root hairs are important for nutrient and water uptake and are also critically involved the interaction with soil inhabiting microbiota. Root hairs are tubular-shaped outgrowths that emerge from trichoblasts. This polarized elongation is maintained and regulated by a robust mechanism involving the endomembrane secretory and endocytic system. Members of the syntaxin family of SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) in plants (SYP), have been implicated in regulation of the fusion of vesicles with the target membranes in both exocytic and endocytic pathways. One member of this family, SYP123, is expressed specifically in the root hairs and accumulated in the growing tip region. This study shows evidence of the SYP123 role in polarized trafficking using knockout insertional mutant plants. We were able to observe defects in the deposition of cell wall proline rich protein PRP3 and cell wall polysaccharides. In a complementary strategy, similar results were obtained using a plant expressing a dominant negative soluble version of SYP123 (SP2 fragment) lacking the transmembrane domain. The evidence presented indicates that SYP123 is also regulating PRP3 protein distribution by recycling by endocytosis. We also present evidence that indicates that SYP123 is necessary for the response of roots to plant growth promoting rhizobacterium (PGPR) in order to trigger trigger induced systemic response (ISR). Plants with a defective SYP123 function were unable to mount a systemic acquired resistance in response to bacterial pathogen infection and ISR upon interaction with rhizobacteria. These results indicated that SYP123 was involved in the polarized localization of protein and polysaccharides in growing root hairs and that this activity also contributed to the establishment of effective plant defense responses. Root hairs represent very plastic structures were many biotic and abiotic factors can affect the number, anatomy and physiology of root hairs. Here, we presented evidence that indicates that interactions with soil PGPR could be closely regulated by signaling involving secretory and/or endocytic trafficking at the root hair tip as a quick way to response to changing environmental conditions.
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http://dx.doi.org/10.3389/fpls.2016.01081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961009PMC
August 2016

The inside and outside: topological issues in plant cell wall biosynthesis and the roles of nucleotide sugar transporters.

Glycobiology 2016 09 9;26(9):913-925. Epub 2016 Aug 9.

Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Avenida República 217, Santiago, RM 837-0146, Chile

The cell wall is a complex extracellular matrix composed primarily of polysaccharides. Noncellulosic polysaccharides, glycoproteins and proteoglycans are synthesized in the Golgi apparatus by glycosyltransferases (GTs), which use nucleotide sugars as donors to glycosylate nascent glycan and glycoprotein acceptors that are subsequently exported to the extracellular space. Many nucleotide sugars are synthesized in the cytosol, leading to a topological issue because the active sites of most GTs are located in the Golgi lumen. Nucleotide sugar transporters (NSTs) overcome this problem by translocating nucleoside diphosphate sugars from the cytosol into the lumen of the organelle. The structures of the cell wall components synthesized in the Golgi are diverse and complex; therefore, transporter activities are necessary so that the nucleotide sugars can provide substrates for the GTs. In this review, we describe the topology of reactions involved in polysaccharide biosynthesis in the Golgi and focus on the roles of NSTs as well as their impacts on cell wall structure when they are altered.
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http://dx.doi.org/10.1093/glycob/cww054DOI Listing
September 2016

The Arabidopsis Golgi-localized GDP-L-fucose transporter is required for plant development.

Nat Commun 2016 07 6;7:12119. Epub 2016 Jul 6.

Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94702, USA.

Nucleotide sugar transport across Golgi membranes is essential for the luminal biosynthesis of glycan structures. Here we identify GDP-fucose transporter 1 (GFT1), an Arabidopsis nucleotide sugar transporter that translocates GDP-L-fucose into the Golgi lumen. Using proteo-liposome-based transport assays, we show that GFT preferentially transports GDP-L-fucose over other nucleotide sugars in vitro, while GFT1-silenced plants are almost devoid of L-fucose in cell wall-derived xyloglucan and rhamnogalacturonan II. Furthermore, these lines display reduced L-fucose content in N-glycan structures accompanied by severe developmental growth defects. We conclude that GFT1 is the major nucleotide sugar transporter for import of GDP-L-fucose into the Golgi and is required for proper plant growth and development.
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http://dx.doi.org/10.1038/ncomms12119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4935801PMC
July 2016

Overview of Nucleotide Sugar Transporter Gene Family Functions Across Multiple Species.

J Mol Biol 2016 08 31;428(16):3150-3165. Epub 2016 May 31.

Centro de Biotecnología Vegetal, Universidad Andres Bello, Av. República 217, Santiago, RM 837-0146, Chile; FONDAP Center for Genome Regulation, Santiago, RM,Chile. Electronic address:

Glycoproteins and glycolipids are crucial in a number of cellular processes, such as growth, development, and responses to external cues, among others. Polysaccharides, another class of sugar-containing molecules, also play important structural and signaling roles in the extracellular matrix. The additions of glycans to proteins and lipids, as well as polysaccharide synthesis, are processes that primarily occur in the Golgi apparatus, and the substrates used in this biosynthetic process are nucleotide sugars. These proteins, lipids, and polysaccharides are also modified by the addition of sulfate groups in the Golgi apparatus in a series of reactions where nucleotide sulfate is needed. The required nucleotide sugar substrates are mainly synthesized in the cytosol and transported into the Golgi apparatus by nucleotide sugar transporters (NSTs), which can additionally transport nucleotide sulfate. Due to the critical role of NSTs in eukaryotic organisms, any malfunction of these could change glycan and polysaccharide structures, thus affecting function and altering organism physiology. For example, mutations or deletion on NST genes lead to pathological conditions in humans or alter cell walls in plants. In recent years, many NSTs have been identified and functionally characterized, but several remain unanalyzed. This study examined existing information on functionally characterized NSTs and conducted a phylogenetic analysis of 257 NSTs predicted from nine animal and plant model species, as well as from protists and fungi. From this analysis, relationships between substrate specificity and the primary NST structure can be inferred, thereby advancing understandings of nucleotide sugar gene family functions across multiple species.
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http://dx.doi.org/10.1016/j.jmb.2016.05.021DOI Listing
August 2016

Identification of Novel Components of the Unfolded Protein Response in Arabidopsis.

Front Plant Sci 2016 12;7:650. Epub 2016 May 12.

Centro de Biotecnología y Genómica de Plantas UPM-INIA, Universidad Politécnica de Madrid Madrid, Spain.

Unfavorable environmental and developmental conditions may cause disturbances in protein folding in the endoplasmic reticulum (ER) that are recognized and counteracted by components of the Unfolded Protein Response (UPR) signaling pathways. The early cellular responses include transcriptional changes to increase the folding and processing capacity of the ER. In this study, we systematically screened a collection of inducible transgenic Arabidopsis plants expressing a library of transcription factors for resistance toward UPR-inducing chemicals. We identified 23 candidate genes that may function as novel regulators of the UPR and of which only three genes (bZIP10, TBF1, and NF-YB3) were previously associated with the UPR. The putative role of identified candidate genes in the UPR signaling is supported by favorable expression patterns in both developmental and stress transcriptional analyses. We demonstrated that WRKY75 is a genuine regulator of the ER-stress cellular responses as its expression was found to be directly responding to ER stress-inducing chemicals. In addition, transgenic Arabidopsis plants expressing WRKY75 showed resistance toward salt stress, connecting abiotic and ER-stress responses.
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http://dx.doi.org/10.3389/fpls.2016.00650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864164PMC
May 2016

PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis.

New Phytol 2016 07;211(1):65-74

Institute of Science and Technology Austria (IST Austria), 3400, Klosterneuburg, Austria.

Plant development mediated by the phytohormone auxin depends on tightly controlled cellular auxin levels at its target tissue that are largely established by intercellular and intracellular auxin transport mediated by PIN auxin transporters. Among the eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate. In this study we generated functional, fluorescent protein-tagged PIN6 proteins and performed comprehensive analysis of their subcellular localization and also performed a detailed functional characterization of PIN6 and its developmental roles. The localization study of PIN6 revealed a dual localization at the plasma membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both auxin transport across the PM and intracellular auxin homeostasis, including the regulation of free auxin and auxin conjugates levels. As evidenced by the loss- and gain-of-function analysis, the complex function of PIN6 in auxin transport and homeostasis is required for auxin distribution during lateral and adventitious root organogenesis and for progression of these developmental processes. These results illustrate a unique position of PIN6 within the family of PIN auxin transporters and further add complexity to the developmentally crucial process of auxin transport.
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http://dx.doi.org/10.1111/nph.14019DOI Listing
July 2016

Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight.

BMC Plant Biol 2016 Apr 26;16:104. Epub 2016 Apr 26.

Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11, 610, Santiago, Chile.

Background: Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6-8 mm berries (B68) phenological stages.

Results: A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles.

Conclusions: We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.
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http://dx.doi.org/10.1186/s12870-016-0789-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4845426PMC
April 2016

Proteomic analysis of a segregant population reveals candidate proteins linked to mealiness in peach.

J Proteomics 2016 Jan 13;131:71-81. Epub 2015 Oct 13.

Universidad Andrés Bello, Fac. Ciencias Biológicas, Centro de Biotecnología Vegetal, República 217, Santiago, Chile; FONDAP-Center of Genome Regulation (CGR), Santiago, Chile.

Peaches are stored at low temperatures to delay ripening and increase postharvest life. However some varieties are susceptible to chilling injury,which leads to fruit mealiness, browning and flesh bleeding. In order to identify potentialmarkers associated with chilling injury,we performed proteomic analyses on a segregating population with contrasting susceptibility to chilling-induced mealiness. Chilling-induced mealiness was assessed by measuring juiciness in fruits that have been stored in cold and then allowed to ripen. Fruitmesocarp and leaf proteome from contrasting segregants were analyzed using 2-DE gels. Comparison of protein abundance between segregants revealed 133 spots from fruit mesocarp and 36 from leaf. Thirty four fruit mesocarp proteins were identified from these spots. Most of these proteins were related to ethylene synthesis, ABA response and stress response. Leaf protein analyses identified 22 proteins, most of which related to energy metabolism. Some of the genes that code for these proteins have been previously correlated with chilling injury through transcript analyses and co-segregation with mealiness QTLs. The results from this study, further deciphers the molecular mechanisms associated with chilling response in peach fruit, and identifies candidate proteins linked to mealiness in peach which may be used as putative markers for this trait.
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http://dx.doi.org/10.1016/j.jprot.2015.10.011DOI Listing
January 2016

The UDP-glucose: glycoprotein glucosyltransferase (UGGT), a key enzyme in ER quality control, plays a significant role in plant growth as well as biotic and abiotic stress in Arabidopsis thaliana.

BMC Plant Biol 2015 May 28;15:127. Epub 2015 May 28.

Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Avenida República 217, Santiago, 837-0146, RM, Chile.

Background: UDP-glucose: glycoprotein glucosyltransferase (UGGT) is a key player in the quality control mechanism (ER-QC) that newly synthesized glycoproteins undergo in the ER. It has been shown that the UGGT Arabidopsis orthologue is involved in ER-QC; however, its role in plant physiology remains unclear.

Results: Here, we show that two mutant alleles in the At1g71220 locus have none or reduced UGGT activity. In wild type plants, the AtUGGT transcript levels increased upon activation of the unfolded protein response (UPR). Interestingly, mutants in AtUGGT exhibited an endogenous up-regulation of genes that are UPR targets. In addition, mutants in AtUGGT showed a 30% reduction in the incorporation of UDP-Glucose into the ER suggesting that this enzyme drives the uptake of this substrate for the CNX/CRT cycle. Plants deficient in UGGT exhibited a delayed growth rate of the primary root and rosette as well as an alteration in the number of leaves. These mutants are more sensitive to pathogen attack as well as heat, salt, and UPR-inducing stressors. Additionally, the plants showed impairment in the establishment of systemic acquired resistance (SAR).

Conclusions: These results show that a lack of UGGT activity alters plant vegetative development and impairs the response to several abiotic and biotic stresses. Moreover, our results uncover an unexpected role of UGGT in the incorporation of UDP-Glucose into the ER lumen in Arabidopsis thaliana.
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http://dx.doi.org/10.1186/s12870-015-0525-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4465474PMC
May 2015

The dynamic of the splicing of bZIP60 and the proteins encoded by the spliced and unspliced mRNAs reveals some unique features during the activation of UPR in Arabidopsis thaliana.

PLoS One 2015 10;10(4):e0122936. Epub 2015 Apr 10.

Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile.

The unfolded protein response (UPR) is a signaling pathway that is activated when the workload of the endoplasmic reticulum (ER) is surpassed. IRE1 is a sensor involved in triggering the UPR and plays a key role in the unconventional splicing of an mRNA leading to the formation of a transcription factor that up-regulates the transcription of genes that play a role in restoring the homeostasis in the ER. In plants, bZIP60 is the substrate for IRE1; however, questions such as what is the dynamics of the splicing of bZIP60 and the fate of the proteins encoded by the spliced and unspliced forms of the mRNA, remain unanswered. In the present work, we analyzed the processing of bZIP60 by determining the levels of the spliced form mRNA in plants exposed to different conditions that trigger UPR. The results show that induction of ER stress increases the content of the spliced form of bZIP60 (bZIP60s) reaching a maximum, that depending on the stimuli, varied between 30 min or 2 hrs. In most cases, this was followed by a decrease in the content. In contrast to other eukaryotes, the splicing never occurred to full extent. The content of bZIP60s changed among different organs upon induction of the UPR suggesting that splicing is regulated differentially throughout the plant. In addition, we analyzed the distribution of a GFP-tagged version of bZIP60 when UPR was activated. A good correlation between splicing of bZIP60 and localization of the protein in the nucleus was observed. No fluorescence was observed under basal conditions, but interestingly, the fluorescence was recovered and found to co-localize with an ER marker upon treatment with an inhibitor of the proteasome. Our results indicate that the dynamics of bZIP60, both the mRNA and the protein, are highly dynamic processes which are tissue-specific and stimulus-dependent.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122936PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393087PMC
March 2016

Comparative study of two table grape varieties with contrasting texture during cold storage.

Molecules 2015 Feb 23;20(3):3667-80. Epub 2015 Feb 23.

Centro de Biotecnología Vegetal, Facultad Ciencias Biológicas, Universidad Andres Bello, República 217, Santiago, Chile.

Postharvest softening of grape berries is one of the main problems affecting grape quality during export. Cell wall disassembly, especially of pectin polysaccharides, has been commonly related to fruit softening, but its influence has been poorly studied in grapes during postharvest life. In order to better understand this process, the Thompson seedless (TS) variety, which has significantly decreased berry texture after prolonged cold storage, was compared to NN107, a new table grape variety with higher berry firmness. Biochemical analysis revealed a greater amount of calcium in the cell wall of the NN107 variety and less reduction of uronic acids than TS during cold storage. In addition, the activity of polygalacturonase was higher in TS than NN107 berries; meanwhile pectin methylesterase activity was similar in both varieties. Polysaccharide analysis using carbohydrate gel electrophoresis (PACE) suggests a differential pectin metabolism during prolonged cold storage. Results revealed lower pectin fragments in TS after 60 days of cold storage and shelf life (SL) compared to 30 days of cold storage and 30 + SL, while NN107 maintained the same fragment profile across all time points evaluated. Our results suggest that these important differences in cell wall metabolism during cold storage could be related to the differential berry firmness observed between these contrasting table grape varieties.
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http://dx.doi.org/10.3390/molecules20033667DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6272506PMC
February 2015

bZIP17 and bZIP60 Regulate the Expression of BiP3 and Other Salt Stress Responsive Genes in an UPR-Independent Manner in Arabidopsis thaliana.

J Cell Biochem 2015 Aug;116(8):1638-45

Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile.

Plants can be severely affected by salt stress. Since these are sessile organisms, they have developed different cellular responses to cope with this problem. Recently, it has been described that bZIP17 and bZIP60, two ER-located transcription factors, are involved in the cellular response to salt stress. On the other hand, bZIP60 is also involved in the unfolded protein response (UPR), a signaling pathway that up-regulates the expression of ER-chaperones. Coincidentally, salt stress produces the up-regulation of BiP, one of the main chaperones located in this organelle. Then, it has been proposed that UPR is associated to salt stress. Here, by using insertional mutant plants on bZIP17 and bZIP60, we show that bZIP17 regulate the accumulation of the transcript for the chaperone BiP3 under salt stress conditions, but does not lead to the accumulation of UPR-responding genes such as the chaperones Calnexin, Calreticulin, and PDIL under salt treatments. In contrast, DTT, a known inducer of UPR, leads to the up-regulation of all these chaperones. On the other hand, we found that bZIP60 regulates the expression of some bZIP17 target genes under conditions were splicing of bZIP60 does not occur, suggesting that the spliced and unspliced forms of bZIP60 play different roles in the physiological response of the plant. Our results indicate that the ER-located transcription factors bZIP17 and bZIP60 play a role in salt stress but this response goes through a signaling pathway that is different to that triggered by the unfolded protein response.
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http://dx.doi.org/10.1002/jcb.25121DOI Listing
August 2015

The Golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of Arabidopsis.

Proc Natl Acad Sci U S A 2014 Aug 22;111(31):11563-8. Epub 2014 Jul 22.

Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago RM 8370146, Chile;Fondo de Areas Prioritarias Center for Genome Regulation, Santiago RM 8370146, Chile;

Plant cells are surrounded by a cell wall that plays a key role in plant growth, structural integrity, and defense. The cell wall is a complex and diverse structure that is mainly composed of polysaccharides. The majority of noncellulosic cell wall polysaccharides are produced in the Golgi apparatus from nucleotide sugars that are predominantly synthesized in the cytosol. The transport of these nucleotide sugars from the cytosol into the Golgi lumen is a critical process for cell wall biosynthesis and is mediated by a family of nucleotide sugar transporters (NSTs). Numerous studies have sought to characterize substrate-specific transport by NSTs; however, the availability of certain substrates and a lack of robust methods have proven problematic. Consequently, we have developed a novel approach that combines reconstitution of NSTs into liposomes and the subsequent assessment of nucleotide sugar uptake by mass spectrometry. To address the limitation of substrate availability, we also developed a two-step reaction for the enzymatic synthesis of UDP-l-rhamnose (Rha) by expressing the two active domains of the Arabidopsis UDP-l-Rha synthase. The liposome approach and the newly synthesized substrates were used to analyze a clade of Arabidopsis NSTs, resulting in the identification and characterization of six bifunctional UDP-l-Rha/UDP-d-galactose (Gal) transporters (URGTs). Further analysis of loss-of-function and overexpression plants for two of these URGTs supported their roles in the transport of UDP-l-Rha and UDP-d-Gal for matrix polysaccharide biosynthesis.
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http://dx.doi.org/10.1073/pnas.1406073111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4128141PMC
August 2014

Using genomics to improve fruit quality.

Biol Res 2013 ;46(4):347-52

New fruit varieties are needed to satisfy consumers, and the industry is facing new challenges in order to respond to these demands. The emergence of genomic tools is releasing information on polymorphisms that can be utilized to expedite breeding processes in species that are difficult to breed, given the long periods of time required to get new varieties. The present review describes the current stages of the ongoing efforts that are being taken to apply these technologies to obtain varieties with improved fruit quality in species of the family Rosaceae.
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http://dx.doi.org/10.4067/S0716-97602013000400006DOI Listing
March 2016

Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants.

BMC Plant Biol 2014 Jan 7;14. Epub 2014 Jan 7.

Fondap Center for Genome Regulation, Av, Blanco Encalada 2085, 3rd floor, Santiago, Chile.

Background: Grapevine (Vitis vinifera L.) is the most important Mediterranean fruit crop, used to produce both wine and spirits as well as table grape and raisins. Wine and table grape cultivars represent two divergent germplasm pools with different origins and domestication history, as well as differential characteristics for berry size, cluster architecture and berry chemical profile, among others. 'Sultanina' plays a pivotal role in modern table grape breeding providing the main source of seedlessness. This cultivar is also one of the most planted for fresh consumption and raisins production. Given its importance, we sequenced it and implemented a novel strategy for the de novo assembly of its highly heterozygous genome.

Results: Our approach produced a draft genome of 466 Mb, recovering 82% of the genes present in the grapevine reference genome; in addition, we identified 240 novel genes. A large number of structural variants and SNPs were identified. Among them, 45 (21 SNPs and 24 INDELs) were experimentally confirmed in 'Sultanina' and six SNPs in other 23 table grape varieties. Transposable elements corresponded to ca. 80% of the repetitive sequences involved in structural variants and more than 2,000 genes were affected in their structure by these variants. Some of these genes are likely involved in embryo development, suggesting that they may contribute to seedlessness, a key trait for table grapes.

Conclusions: This work produced the first structural variants and SNPs catalog for grapevine, constituting a novel and very powerful tool for genomic studies in this key fruit crop, particularly useful to support marker assisted breeding in table grapes.
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http://dx.doi.org/10.1186/1471-2229-14-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890619PMC
January 2014

Identification of two putative reference genes from grapevine suitable for gene expression analysis in berry and related tissues derived from RNA-Seq data.

BMC Genomics 2013 Dec 13;14:878. Epub 2013 Dec 13.

Instituto de Investigaciones Agropecuarias (INIA -Chile), La Platina Research Centre, Santiago, Chile, Av, Santa Rosa 11, 610, P,O, Box 439-3, Santiago, Chile.

Background: Data normalization is a key step in gene expression analysis by qPCR. Endogenous control genes are used to estimate variations and experimental errors occurring during sample preparation and expression measurements. However, the transcription level of the most commonly used reference genes can vary considerably in samples obtained from different individuals, tissues, developmental stages and under variable physiological conditions, resulting in a misinterpretation of the performance of the target gene(s). This issue has been scarcely approached in woody species such as grapevine.

Results: A statistical criterion was applied to select a sub-set of 19 candidate reference genes from a total of 242 non-differentially expressed (NDE) genes derived from a RNA-Seq experiment comprising ca. 500 million reads obtained from 14 table-grape genotypes sampled at four phenological stages. From the 19 candidate reference genes, VvAIG1 (AvrRpt2-induced gene) and VvTCPB (T-complex 1 beta-like protein) were found to be the most stable ones after comparing the complete set of genotypes and phenological stages studied. This result was further validated by qPCR and geNorm analyses.

Conclusions: Based on the evidence presented in this work, we propose to use the grapevine genes VvAIG1 or VvTCPB or both as a reference tool to normalize RNA expression in qPCR assays or other quantitative method intended to measure gene expression in berries and other tissues of this fruit crop, sampled at different developmental stages and physiological conditions.
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http://dx.doi.org/10.1186/1471-2164-14-878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878734PMC
December 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