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José Tomás Matus

José Tomás Matus
Institute for Integrative Systems Biology (I2SysBio) · Systems Biology of Molecular Interactions and Regulation

Biology BSc, PhD in Agricultural Sciences.

About

79
Publications
26,750
Reads
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2,466
Citations
Introduction
PI at Institute for Integrative Systems Biology (I2SysBio), València
Additional affiliations
April 2019 - present
Instituto de Biología Integrativa de Sistemas
Position
  • PI
Description
  • PI of TomsBioLab (http://tomsbiolab.com)
May 2015 - April 2019
CRAG Centre for Research in Agricultural Genomics
Position
  • PostDoc Position
October 2014 - July 2015
Centro de Investigación e Innovación Concha y Toro
Position
  • Consultant
Education
March 1998 - August 2003

Publications

Publications (79)
Article
Full-text available
Due to the vast range of functions that phenylpropanoids possess, their synthesis requires precise spatio-temporal coordination throughout plant development and in response to the environment. The accumulation of these secondary metabolites is transcriptionally controlled by positive and negative regulators from the MYB and bHLH protein families. W...
Article
Full-text available
R2R3-MYB transcription factors (TFs) belong to a large and functionally diverse protein superfam-ily in plants. In this study, we explore the evolution and function of this family in grapevine (Vitis vinifera L.), a high-value fruit crop. We identified and manually curated 134 genes using RNA-Seq data, and named them systematically according to the...
Article
Full-text available
Grapevine (Vitis vinifera L.) is a species well known for its adaptation to radiation. However, photomorphogenic factors related to UV-B responses have not been molecularly characterized. We cloned and studied the role of UV-B RECEPTOR (UVR1), ELONGATED HYPOCOTYL 5 (HY5), and HY5 HOMOLOGUE (HYH) from V. vinifera. We performed gene functional charac...
Article
Grapevine organs accumulate anthocyanins in a cultivar-specific and environmentally induced manner. The MYBA1-A2 genes within the berry color locus in chromosome 2 represent the major genetic determinants of fruit color. The simultaneous occurrence of transposon insertions and point mutations in these genes is responsible for most white-skinned phe...
Article
Full-text available
We explored the effects of ultraviolet B radiation (UV-B) on the developmental dynamics of microRNAs and phased small-interfering-RNA (phasi-RNAs)-producing loci by sequencing small RNAs in vegetative and reproductive organs of grapevine (Vitis vinifera L.). In particular, we tested different UV-B conditions in in vitro-grown plantlets (high-fluenc...
Article
Full-text available
Successfully integrating transcriptomic experiments is a challenging task with the ultimate goal of analyzing gene expression data in the broader context of all available measurements, all from a single point of access. In its second major release VESPUCCI, the integrated database of gene expression data for grapevine, has been updated to be FAIR-c...
Article
Full-text available
The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators of this pathway but the extent of this control has not been deeply studied. Here we demonstrate how DNA affinity purification sequencing (DAP‐Seq) allows for genome‐wide TF bi...
Article
Full-text available
Effective crop improvement, whether through selective breeding or biotech strategies, is largely dependent on the cumulative knowledge of a species’ pangenome and its containing genes. Acquiring this knowledge is specially challenging in grapevine, one of the oldest fruit crops grown worldwide, which is known to have more than 30,000 genes. Well-es...
Preprint
Full-text available
The presence of naturally-occurring color mutants in plants has permitted the identification of many regulatory genes implicated in the synthesis of discrete metabolic compounds, mostly anthocyanins and carotenoids. Conversely, transcription factors that coordinate more than one specialized metabolic pathway seem challenging to screen from a forwar...
Article
Full-text available
The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obt...
Preprint
Grapevine is a woody temperate perennial plant and one of the most important fruit crops with global relevance in both the fresh fruit and winemaking industries. Unfortunately, global warming is affecting viticulture by altering developmental transitions and fruit maturation processes. In this context, uncovering the molecular mechanisms controllin...
Preprint
PHYTOCHROME INTERACTING FACTORs (PIFs) are transcription factors that interact with the photoreceptors phytochromes and integrate multiple signaling pathways related to light, temperature, defense and hormone responses. PIFs have been extensively studied in Arabidopsis thaliana, but less is known about their roles in other species. Here, we investi...
Article
Full-text available
Main conclusion White-fleshed grape cv. ‘Gamay’ and its two teinturier variants presented distinct spatial–temporal accumulation of anthocyanins, with uncoupled accumulation of sugars and anthocyanins in ‘Gamay Fréaux’. AbstractIn most red grape cultivars, anthocyanins accumulate exclusively in the berry skin, while ‘teinturier’ cultivars also accu...
Preprint
Full-text available
The stilbenoid pathway is responsible for the production of resveratrol and its derivatives in grapevine. A few transcription factors (TFs) have been previously identified as regulators of this pathway but the extent of this control is yet to be fully understood. Here we demonstrate how DNA affinity purification sequencing (DAP-Seq) allows for geno...
Article
Full-text available
Carotenoids are essential components of the photosynthetic antenna and reaction center complexes, being also responsible for antioxidant defense, coloration, and many other functions in multiple plant tissues. In tomato, salinity negatively affects the development of vegetative organs and productivity, but according to previous studies it might als...
Article
Plastids, the defining organelles of plant cells, undergo physiological and morphological changes to fulfill distinct biological functions. In particular, the differentiation of chloroplasts into chromoplasts results in an enhanced storage capacity for carotenoids with industrial and nutritional value such as beta-carotene (provitamin A). Here, we...
Article
Cannabis sativa is a source of food, fiber and specialized metabolites such as cannabinoids, with psychoactive and pharmacological effects. Due to its expanding and increasingly-accepted use in medicine, cannabis cultivation is acquiring more importance and less social stigma. Humans initiated different domestication episodes whose later spread gav...
Article
Full-text available
Background: Somatic mutations occurring within meristems of vegetative propagation material have had a major role in increasing the genetic diversity of the domesticated grapevine (Vitis vinifera subsp. vinifera). The most well studied somatic variation in this species is the one affecting fruit pigmentation, leading to a plethora of different ber...
Preprint
Full-text available
Anthocyanins are flavonoids responsible for the color of berries in skin-pigmented grapevine (Vitis vinifera L.). Due to the widely adopted vegetative propagation of this species, somatic mutations occurring in meristematic cell layers can be fixed and passed into the rest of the plant when cloned. In this study we focused on the transcriptomic and...
Chapter
The cultivated grapevine, Vitis vinifera L., has gathered a vast amount of omics data throughout the last two decades, driving the imperative use of computational resources for its analysis and integration. Molecular systems biology arises from this need allowing to model and predict the emergence of phenotypes or responses in biological systems. B...
Preprint
Full-text available
UV-B regulation of anthocyanin biosynthesis in vegetative and grapevine berry tissues has been extensively described. However, its relation with UV-B-regulated microRNAs (miRNAs) has not been addressed before in this species. We explored by deep sequencing of small RNA libraries the developmental dynamics and UV-B effects on miRNAs and associated p...
Article
Full-text available
Stilbene synthase (STS) is the key enzyme leading to the biosynthesis of resveratrol. Recently we reported two R2R3-MYB transcription factors (TFs) that regulate the stilbene biosynthetic pathway in grapevine: VviMYB14 and VviMYB15. These genes strongly co-express with STSs under a range of stress and developmental conditions, in agreement with the...
Article
Full-text available
Grapevine (Vitis vinifera L.) is a widely cultivated fruit crop whose growth and productivity are largely affected by low temperatures. On the other hand, wild Vitis species represent valuable genetic resources of natural stress tolerance. We have isolated and characterized a MYB-like gene encoding a putative GARP-type transcription factor from Amu...
Article
Full-text available
Flavonols constitute a group of flavonoids with important photoprotective roles in plants. In addition, flavonol content and composition greatly influences fruit quality. We previously demonstrated that the grapevine R2R3-MYB transcription factor (TF) VviMYBF1 promotes flavonol accumulation by inducing the expression of flavonol synthase (VviFLS1/V...
Article
Full-text available
Representing large biological data as networks is becoming increasingly adopted for predicting gene function while elucidating the multifaceted organization of life processes. In grapevine (Vitis vinifera L.), network analyses have been mostly adopted to contribute to the understanding of the regulatory mechanisms that control berry composition. Wh...
Article
Full-text available
Plants are constantly challenged by environmental fluctuations. In response, they have developed a wide range of morphological and biochemical adaptations committed to ameliorate the effects of abiotic stress. When exposed to higher solar radiation levels, plants activate the synthesis of a large set of enzymes and secondary metabolites as part of...
Article
Shoot apical meristem activity is controlled by complex regulatory networks in which components such as transcription factors, miRNAs, small peptides, hormones, enzymes and epigenetic marks all participate. Many key genes that determine the inherent characteristics of the shoot apical meristem have been identified through genetic approaches. Recent...
Article
Full-text available
The RESPONSIVE TO DEHYDRATION 22 (RD22) gene is a molecular link between abscisic acid (ABA) signalling and abiotic stress responses. Its expression has been used as a reliable ABA early response marker. In Arabidopsis, the single copy RD22 gene possesses a BURP domain also located at the C-terminus of USP embryonic proteins and the beta subunit of...
Article
Full-text available
Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression o...
Article
Determining gene function through reverse genetics has been an important experimental approach in the field of flower development. The method largely relies on the availability of knockout lines for the gene of interest. Insertional mutagenesis can be performed using either T-DNA or transposable elements, but the former has been more frequently emp...
Data
Post-veraison sunlight exposure induces MYB-mediated transcriptional regulation of anthocyanin and flavonol synthesis in berry skins of Vitis vinifera. J Exp Bot. 2009;60(3):853-67. Supplementary Video S1 Daily time course of the experimental field in which sunlight treatments were imposed (north orientation). In each row, all treatments were appl...
Data
Occurrence of [A/T]AAAG motifs in the 300 bp regulatory region located upstream of the translational start codon of the AtMYB60, VvMYB30, VvMYB60 and VvSIRK genes. [A/T]AAAG nucleotides on the + strand are highlighted in yellow, whereas [A/T]AAAG nucleotides on the - strand are highlighted in pale blue. The predicted TATA box is in italic and highl...
Data
Deduced gene structure of AtMYB60, VvMYB30 and VvMYB60. Boxes represent exons, while black lines represent introns. The location of the ATG start codon is indicated (black arrow). Gene organization and size of exons and introns were deduced by comparing the sequence of amplified genomic and cDNA fragments. Yellow and green boxes represent exon sequ...
Data
Activity of the grape VvMYB360 and VvMYB60 promoters in flowers and siliques from Arabidopsis lines carrying promoter:GUS fusions. (A) GUS expression in pVvMYB30:GUS flowers was localized in carpels and stigmatic tissues (arrow). (B) Most pVvMYB60:GUS flowers did not show GUS activity, with the exception of two independent lines which disclosed sta...
Data
Phenotypic changes in grapevine plantlets grown in the presence of growing NaCl concentration. Pictures were taken one month after the beginning of the treatment.
Data
Generation and selection of the transgenic lines used for the complementation of the atmyb60-1 Arabidopsis mutant (atmyb60-C60 and atmyb60-C30). (A) and (B), schematic representation of the constructs used in the complementation test (not to scale). (C) and (D), RT-PCR analysis of transgene expression (VvMYB60 and VvMYB30) in three independent homo...
Article
Full-text available
Under drought, plants accumulate the signaling hormone abscisic acid (ABA), which induces the rapid closure of stomatal pores to prevent water loss. This event is trigged by a series of signals produced inside guard cells which finally reduce their turgor. Many of these events are tightly regulated at the transcriptional level, including the contro...
Chapter
Full-text available
Although the flowering process in herbaceous species has been well characterized, the genetic, hormonal and environmental factors regulating flower development in fruit crop species are far from being elucidated. Grapevine (Vitis vinifera L.) is a woody plant belonging to the Core Eudicots, with significant agricultural importance. The reproductive...
Article
Arabidopsis genomic and network analyses have facilitated crop research towards the understanding of many biological processes of fundamental importance for agriculture. Genes that were identified through genomic analyses in Arabidopsis have been used to manipulate crop traits such as pathogen resistance, yield, water-use efficiency, and drought to...
Article
Full-text available
Anthocyanins and tannins are two of the most abundant flavonoids found in grapevine, and their synthesis is derived from the phenylpropanoid pathway. As described for model species such as Arabidopsis thaliana, maize and petunia, the end-point branches of this pathway are tightly regulated by the combinatorial interaction of three families of regul...
Article
Full-text available
Anthocyanins, flavan-3-ols, and flavonols are the three major classes of flavonoid compounds found in grape berry tissues. Several viticultural practices increase flavonoid content in the fruit, but the underlying genetic mechanisms responsible for these changes have not been completely deciphered. The impact of post-veraison sunlight exposure on a...
Article
Full-text available
A new and devastating physiological disorder of Vitis vinifera cv. Merlot was recently reported, known as premature berry dehydration (PBD), which is characterized by plant growth reduction, induction of general senescence and pedicel necrosis in the fruit, causing significant reductions in vineyard production. The causes of this disease remain unc...
Article
Full-text available
In their letter, Storey et al. (1) concede that there is no direct genetic support for Polynesian–South American contact. However, they claim that linguistic, archaeological, and ethnohistoric evidence supports Polynesia as the most likely source of the El Arenal-1 chickens. We disagree on two grounds. First, such indirect evidence is conjectural,...
Article
A new and devastating physiological disorder of Vitis vinifera cv. Merlot was recently reported, known as premature berry dehydration (PBD), which is characterized by plant growth reduction, induction of general senescence and pedicel necrosis in the fruit, causing significant reductions in vineyard production. The causes of this disease remain unc...
Article
Full-text available
Viral infections and their spread throughout a plant require numerous interactions between the host and the virus. While new functions of viral proteins involved in these processes have been revealed, current knowledge of host factors involved in the spread of a viral infection is still insufficient. In Arabidopsis thaliana, different ecotypes pres...
Article
Full-text available
European chickens were introduced into the American continents by the Spanish after their arrival in the 15th century. However, there is ongoing debate as to the presence of pre-Columbian chickens among Amerindians in South America, particularly in relation to Chilean breeds such as the Araucana and Passion Fowl. To understand the origin of these p...
Data
Complete phylogenetic tree of Vitis and Arabidopsis MYB proteins, using the DNA-binding domain (A) or full protein sequences (B). The Neighbour Joining (NJ) tree method was used. Numbers above nodes represent bootstrap values for 2000 replicates. Asterisks indicate Vitis-specific gene pairs and red and blue letters next to gene model identifiers re...
Data
Full-text available
Selected candidate grape MYB genes and PCR primers used for isolation and real-time Q-PCR.
Data
Three dimensional modelling of grape MYB R2R3 domains. A) Vitis and Arabidopsis genes were aligned with the Ratus c-MYB R2R3 domain using the ClustalW module (VECTOR NTI, Invitrogen). Identical amino acid residues are shaded in yellow, and bars indicate the positions of the three α-helices from each repeat. The six asterisks indicate the constantly...
Data
Phylogenetic tree of the Vitis , Arabidopsis and Rice R2R3 MYB Subfamily. The R2R3 DNA-binding domain sequences were used for the construction of a parsimony phylogeny tree with Mega4 software using the Neighbour Joining (NJ) tree method. Numbers above nodes represent bootstrap values for 2000 replicates.
Data
Affymetrix (ATH1 Gene Chip) MYB expression data during Arabidopsis organ development from the putative homologues of the selected grape genes. Data was collected using the Arabidopsis Electronic Fluorescent Pictograph (eFP) Browser. Colours refer to an absolute expression unit, calculated independently for each gene and normalised by the RMA or GCO...
Data
Multiple alignment of 20 representative R2R3 MYB domains from Arabidopsis and six MYB domains from characterised grape MYB genes. Identical amino acid residues are shaded in yellow and the blue and white boxes indicate the extent of the R2 and R3 repeats. The consensus sequence shown under the alignment was used to search for MYB homologues in the...
Data
Full-text available
List of R2R3 MYB gene models in the Grape Genome with their predicted orthologues in sequenced plant species and exon lengths.
Data
Full-text available
List of R2R3 MYB genes in the Arabidopsis Genome, including their chromosome positions and protein and exon lengths. AtMYB88 and AtMYB124 are highlighted since they possess 10 and 11 exons, respectively and only the first five exons appear in the table.