Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Genomic Origin and Diversification of the Glucosinolate MAM Locus
    Abrahams, R.S. ; Pires, J.C. ; Schranz, M.E. - \ 2020
    Frontiers in Plant Science 11 (2020). - ISSN 1664-462X
    brassicaceae - gene duplication - gene family - gene fusion - glucosinolates - polyploidy

    Glucosinolates are a diverse group of plant metabolites that characterize the order Brassicales. The MAM locus is one of the most significant QTLs for glucosinolate diversity. However, most of what we understand about evolution at the locus is focused on only a few species and not within a phylogenetic context. In this study, we utilize a micro-synteny network and phylogenetic inference to investigate the origin and diversification of the MAM/IPMS gene family. We uncover unique MAM-like genes found at the orthologous locus in the Cleomaceae that shed light on the transition from IPMS to MAM. In the Brassicaceae, we identify six distinct MAM clades across Lineages I, II, and III. We characterize the evolutionary impact and consequences of local duplications, transpositions, whole genome duplications, and gene fusion events, generating several new hypothesizes on the function and diversity of the MAM locus.

    On the Origin of SERKs: Bioinformatics Analysis of the Somatic Embryogenesis Receptor Kinases
    Toorn, M. aan den; Albrecht, C. ; Vries, S.C. de - \ 2015
    Molecular Plant 8 (2015)5. - ISSN 1674-2052 - p. 762 - 782.
    epidermal-growth-factor - leucine-rich repeat - molecular characterization - evolutionary conservation - expression analysis - gene family - phosphorylation sites - duplicated genes - protein-kinases - arabidopsis
    Somatic embryogenesis receptor-like kinases (SERKs) are leucine-rich repeat receptor-like kinases involved in several, seemingly unrelated, plant-signaling pathways. In Arabidopsis thaliana, functional and genetic analysis of four SERK proteins has indicated that they are only partly redundant; their functions overlap but each performs a specific subset of signaling roles. The molecular basis for the functional specificity within this highly homologous protein family is currently not known. Sequence analysis of SERK proteins from different plant species indicates that the SERKs are a highly conserved protein family present in monocots, dicots, and non-vascular plants. Residues in the extracellular domain that are important for interaction with other receptor kinases are highly conserved, even among SERK members without a function in the corresponding pathways. SERK2, for instance, does not function in the brassinosteroid pathway, does not interact with BRI1, but is conserved in its BRI1-interacting domain. Further sequence analysis indicates that SERK3/BAK1 and SERK4/BKK1 have diverged from the original SERK protein in both their extracellular and cytoplasmic domains. Functional analysis of chimeric SERK proteins shows that different domains provide the SERK proteins with different functional specificity. For instance, the SERK1 or SERK2 extracellular domains are essential for SERK function in male sporogenesis, while the SERK3 extracellular and cytoplasmic domains are essential for SERK3 activity in brassinosteroid and flagellin signaling. The emerging picture is that SERKs are ancient genes, whose products have been recruited as co-receptors in the newly evolved signaling pathways. The SERK ligand-binding and protein–protein interaction domains are highly conserved, allowing all SERKs to form complexes, albeit with different affinity. However, specific functional residues must have been altered, in both the extracellular and intracellular domains, to allow for the observed differences in functionality.
    Molecular and functional characterization of the scavenger receptor CD36 in zebrafish and common carp
    Fink, I.R. ; Benard, E.L. ; Hermsen, G.J. ; Meijer, A.H. ; Forlenza, M. ; Wiegertjes, G. - \ 2015
    Molecular Immunology 63 (2015)2. - ISSN 0161-5890 - p. 381 - 393.
    toll-like receptors - salmon salmo-salar - cyprinus-carpio - density-lipoprotein - neutrophilic granulocytes - monoclonal-antibodies - accessory molecules - innate immunity - gene family - in-vivo
    CD36 is a scavenger receptor which has been studied closely in mammals where it is expressed by many different cell types and plays a role in highly diverse processes, both homeostatic and pathologic. It is among other things important in the innate immune system, in angiogenesis, and in clearance of apoptotic cells, and it is also involved in lipid metabolism and atherosclerosis. Recently, in the cephalochordate amphioxus a primitive CD36 family member was described, which was present before the divergence of CD36 from other scavenger receptor B family members, SCARB1 and SCARB2. Not much is known on the Cd36 molecule in teleost fish. We therefore studied Cd36 in both zebrafish and common carp, two closely related cyprinid fish species. Whereas a single cd36 gene is present in zebrafish, carp has two cd36 genes, and all show conserved synteny compared to mammalian CD36. The gene expression of carp cd36 is high in brain, ovary and testis but absent in immune organs. Although in mammals CD36 expression in erythrocytes, monocytes and macrophages is high, gene expression studies in leukocyte subtypes of adult carp and zebrafish larvae, including thrombocytes and macrophages provided no indication for any substantial expression of cd36 in immune cell types. Surprisingly, analysis of the cd36 promoter region does show the presence of several binding sites for transcription factors known to regulate immune responses. Overexpression of carp cd36 locates the receptor on the cell surface of mammalian cell lines consistent with the predicted topology of cyprinid Cd36 with a large extracellular domain, two transmembrane domains, and short cytoplasmic tails at both ends. Gene expression of cd36 is down-regulated during infection of zebrafish with Mycobacterium marinum, whereas knockdown of cd36 in zebrafish larvae led to higher bacterial burden upon such infection. We discuss the putative role for Cd36 in immune responses of fish in the context of other members of the scavenger receptor class B family.
    Characterization of a Putative Serk-Like Ortholog in Embryogenic Cell Suspension Cultures of Coffea arabica L.
    Silva, A.T. ; Barduche, D. ; Livramento, K.G. do; Ligterink, W. ; Pavia, L.V. - \ 2014
    Plant Molecular Biology Reporter 32 (2014)1. - ISSN 0735-9640 - p. 176 - 184.
    receptor-like kinases - leucine-rich repeat - somatic-embryogenesis - plant development - molecular characterization - phylogenetic trees - gene family - expression - identification - competence
    The acquisition of embryogenic cell suspension cultures (ECS) has been the objective of studies on in vitro induction of somatic embryogenesis with biotechnological tools, due to the high efficiency of ECS as plant material for genetic transformation and large-scale production and cryopreservation of germplasm. The objective of this work was to identify and analyze one of the main gene families involved in somatic embryogenesis, somatic embryogenesis receptor-like kinase (SERK) in coffee (Coffea arabica L.). Coffee SERKs were identified by searching an EST (expression sequences tag) database generated by the Brazilian Coffee Genome Project starting from candidate sequences obtained from the NCBI database (National Center for Biotechnology Information) . In silico analysis and quantitative PCR results imply that the identified EST-contig C166 might directly be involved in somatic embryogenesis. The results suggest that C166 is the possible ortholog of SERK in C. arabica (CaSERK) and indicate that C166 might be a valuable bio-marker for ECS, and in that context can increase the methodological efficiency for ECS formation in C. arabica. Functional analysis of CaSERK with mutants of a more manageable species will lead to a better understanding of the molecular regulation as well as the specific functions of genes involved in somatic embryogenesis in coffee
    Antiphase light and temperature cycles affect PHYTOCHROME B-controlled ethylene sensitivity and biosynthesis, limiting leaf movement and growth of Arabidopsis.
    Bours, R.M.E.H. ; Zanten, M. van; Pierik, R. ; Bouwmeester, H.J. ; Krol, A.R. van der - \ 2013
    Plant Physiology 163 (2013)2. - ISSN 0032-0889 - p. 882 - 895.
    gene family - thermoperiodic responses - night temperature - circadian-rhythms - identify ethylene - stem elongation - thaliana - gibberellins - morphology - mutations
    In the natural environment, days are generally warmer than the night, resulting in a positive day/night temperature difference (+DIF). Plants have adapted to these conditions, and when exposed to antiphase light and temperature cycles (cold photoperiod/warm night [-DIF]), most species exhibit reduced elongation growth. To study the physiological mechanism of how light and temperature cycles affect plant growth, we used infrared imaging to dissect growth dynamics under +DIF and -DIF in the model plant Arabidopsis (Arabidopsis thaliana). We found that -DIF altered leaf growth patterns, decreasing the amplitude and delaying the phase of leaf movement. Ethylene application restored leaf growth in -DIF conditions, and constitutive ethylene signaling mutants maintain robust leaf movement amplitudes under -DIF, indicating that ethylene signaling becomes limiting under these conditions. In response to -DIF, the phase of ethylene emission advanced 2 h, but total ethylene emission was not reduced. However, expression analysis on members of the 1-aminocyclopropane-1-carboxylic acid (ACC) synthase ethylene biosynthesis gene family showed that ACS2 activity is specifically suppressed in the petiole region under -DIF conditions. Indeed, petioles of plants under -DIF had reduced ACC content, and application of ACC to the petiole restored leaf growth patterns. Moreover, acs2 mutants displayed reduced leaf movement under +DIF, similar to wild-type plants under -DIF. In addition, we demonstrate that the photoreceptor PHYTOCHROME B restricts ethylene biosynthesis and constrains the -DIF-induced phase shift in rhythmic growth. Our findings provide a mechanistic insight into how fluctuating temperature cycles regulate plant growth.
    Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.)
    Visioni, A. ; Tondelli, A. ; Francia, E. ; Pswarayi, A. ; Malosetti, M. ; Russell, J. ; Thomas, W. ; Waugh, R. ; Pecchioni, N. ; Romagosa, I. ; Comadran, J. - \ 2013
    BMC Genomics 14 (2013). - ISSN 1471-2164 - 13 p.
    low-temperature tolerance - linkage disequilibrium - freezing tolerance - gene family - locus - vernalization - population - winterhardiness - components - adaptation
    Background: Frost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure. Results: GWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress Conclusions: Haplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance
    Ve1-mediated resistance against Verticillium does not involve a hypersensitive response in Arabidopsis
    Zhang, Z. ; Esse, H.P. van; Damme, M. van; Fradin, E.F. ; Liu, Chun-Ming ; Thomma, B.P.H.J. - \ 2013
    Molecular Plant Pathology 14 (2013)7. - ISSN 1464-6722 - p. 719 - 727.
    ethylene-inducing xylanase - receptor-like proteins - gated ion-channel - disease resistance - rhynchosporium-secalis - functional-analysis - defense responses - gene family - tomato ve1 - cell-death
    The recognition of pathogen effectors by plant immune receptors leads to the activation of immune responses that often include a hypersensitive response (HR): rapid and localized host cell death surrounding the site of attempted pathogen ingress. We have demonstrated previously that the recognition of the Verticillium dahliae effector protein Ave1 by the tomato immune receptor Ve1 triggers an HR in tomato and tobacco. Furthermore, we have demonstrated that tomato Ve1 provides Verticillium resistance in Arabidopsis upon Ave1 recognition. In this study, we investigated whether the co-expression of Ve1 and Ave1 in Arabidopsis results in an HR, which could facilitate a forward genetics screen. Surprisingly, we found that the co-expression of Ve1 and Ave1 does not induce an HR in Arabidopsis. These results suggest that an HR may occur as a consequence of Ve1/Ave1-induced immune signalling in tomato and tobacco, but is not absolutely required for Verticillium resistance.
    Neuroendocrine-immune interaction: regulation of inflammation via G-protein coupled receptors
    Verburg-van Kemenade, B.M.L. ; Aa, L.M. van der; Chadzinska, M.K. - \ 2013
    General and Comparative Endocrinology 188 (2013). - ISSN 0016-6480 - p. 94 - 101.
    cyprinus-carpio l. - toll-like receptors - common carp - chemokine receptor - cxc chemokine - expression analysis - innate immunity - teleost fish - gene family - in-vivo
    Neuroendocrine- and immune systems interact in a bi-directional fashion to communicate the status of pathogen recognition to the brain and the immune response is influenced by physiological changes. The network of ligands and their receptors involved includes cytokines and chemokines, corticosteroids, classical pituitary hormones, catecholamines and neuropeptides (e.g. opioids), as well as neural pathways. We studied the role of opioid, adrenergic and melatonin G-protein coupled receptors (GPCR) on carp (Cyprinus carpio) leucocytes. Ligand interaction by morphine and adrenaline both in vitro and in vivo resulted in considerable decrease of chemotaxis and expression of CXC chemokines and chemokine CXC receptors. These effects may have substantial influence on the process of inflammation, the efficacy of which is crucial for an effective immune response. Both opioid receptors and chemokine receptors are G-protein coupled receptors (GPCRs), and were classically assumed to function as monomers. This paradigm is now challenged by the emerging concept of homo- and hetero dimerization which may represent the native form of many receptors. G-protein coupling, downstream signaling and regulatory processes such as receptor internalization are largely influenced by the dimeric nature. The true functional importance of GPCR interactions remains enigmatic, but it certainly has implications with respect to the specificity of currently used medications. This review focuses on the important function of chemokine GPCRs during inflammation and the potential neuroendocrine modulation of this process through “neuroendocrine” GPCRs.
    A PHABULOSA/Cytokinin feedback loop controls root growth in Arabidopsis
    Dello loio, R. ; Galinha, C. ; Fletcher, A.G. ; Grigg, S.P. ; Molnar, A. ; Willemsen, V. ; Scheres, B. - \ 2012
    Current Biology 22 (2012)18. - ISSN 0960-9822 - p. 1699 - 1704.
    stem-cell niche - gene family - cytokinin - meristem - auxin - differentiation - expression - polarity - biosynthesis - nitrate
    The hormone cytokinin (CK) controls root length in Arabidopsis thaliana by defining where dividing cells, derived from stem cells of the root meristem, start to differentiate. However, the regulatory inputs directing CK to promote differentiation remain poorly understood. Here, we show that the HD-ZIPIII transcription factor PHABULOSA (PHB) directly activates the CK biosynthesis gene ISOPENTENYL TRANSFERASE 7 (IPT7), thus promoting cell differentiation and regulating root length. We further demonstrate that CK feeds back to repress both PHB and microRNA165, a negative regulator of PHB. These interactions comprise an incoherent regulatory loop in which CK represses both its activator and a repressor of its activator. We propose that this regulatory circuit determines the balance of cell division and differentiation during root development and may provide robustness against CK fluctuations.
    A petunia ABC protein controls strigolactone-dependent symbiotic signalling and branching
    Kretzschmar, T. ; Kohlen, W. ; Sasse, J. ; Borghi, L. ; Schlegel, M. ; Bachelier, J.B. ; Reinhardt, D. ; Bours, R.M.E.H. ; Bouwmeester, H.J. ; Martinoia, E. - \ 2012
    Nature 483 (2012)7389. - ISSN 0028-0836 - p. 341 - 344.
    arbuscular-mycorrhizal fungi - medicago-truncatula - auxin transport - abscisic-acid - gene family - arabidopsis - pcr - germination - inhibition - pathway
    Strigolactones were originally identified as stimulators of the germination of root-parasitic weeds1 that pose a serious threat to resource-limited agriculture2. They are mostly exuded from roots and function as signalling compounds in the initiation of arbuscular mycorrhizae3, which are plant–fungus symbionts with a global effect on carbon and phosphate cycling4. Recently, strigolactones were established to be phytohormones that regulate plant shoot architecture by inhibiting the outgrowth of axillary buds5, 6. Despite their importance, it is not known how strigolactones are transported. ATP-binding cassette (ABC) transporters, however, are known to have functions in phytohormone translocation7, 8, 9. Here we show that the Petunia hybrida ABC transporter PDR1 has a key role in regulating the development of arbuscular mycorrhizae and axillary branches, by functioning as a cellular strigolactone exporter. P. hybrida pdr1 mutants are defective in strigolactone exudation from their roots, resulting in reduced symbiotic interactions. Above ground, pdr1 mutants have an enhanced branching phenotype, which is indicative of impaired strigolactone allocation. Overexpression of Petunia axillaris PDR1 in Arabidopsis thaliana results in increased tolerance to high concentrations of a synthetic strigolactone, consistent with increased export of strigolactones from the roots. PDR1 is the first known component in strigolactone transport, providing new opportunities for investigating and manipulating strigolactone-dependent processes.
    Exploiting an ancient signalling machinery to enjoy a nitorgen fixing symbiosis
    Geurts, R. ; Lillo, A. ; Bisseling, T. - \ 2012
    Current Opinion in Plant Biology 15 (2012)4. - ISSN 1369-5266 - p. 438 - 443.
    receptor-like kinases - medicago-truncatula - lotus-japonicus - arbuscular mycorrhiza - dna-sequences - gene family - 3 genomes - evolution - bacteria - pathway
    For almost a century now it has been speculated that a transfer of the largely legume-specific symbiosis with nitrogen fixing rhizobium would be profitable in agriculture [ [1] and [2]]. Up to now such a step has not been achieved, despite intensive research in this era. Novel insights in the underlying signalling networks leading to intracellular accommodation of rhizobium as well as mycorrhizal fungi of the Glomeromycota order show extensive commonalities between both interactions. As mycorrhizae symbiosis can be established basically with most higher plant species it raises questions why is it only in a few taxonomic lineages that the underlying signalling network could be hijacked by rhizobium. Unravelling this will lead to insights that are essential to achieve an old dream
    A phylogenetic strategy based on a legume-specific whole genome duplication yields symbiotic cytokinin type-A Response Regulators
    Camp, R. Op den; Mita, S. De; Lillo, A. ; Cao, Q. ; Limpens, E.H.M. ; Bisseling, T. ; Geurts, R. - \ 2011
    Plant Physiology 157 (2011)4. - ISSN 0032-0889 - p. 2013 - 2022.
    lateral root-formation - nodule organogenesis - medicago-truncatula - lotus-japonicus - signal-transduction - diverse roles - white clover - gene family - arabidopsis - nodulation
    Legumes host their rhizobium symbiont in novel root organs, called nodules. Nodules originate from differentiated root cortical cells that de-differentiate and subsequently form nodule primordia, a process controlled by cytokinin. A whole genome duplication (WGD) has occurred at the root of the legume Papilionoideae subfamily. We hypothesize that gene pairs originating from this duplication event and are conserved in distinct Papilionoideae lineages have evolved symbiotic functions. A phylogenetic strategy was applied to search for such gene pairs in order to identify novel regulators of nodulation, using the cytokinin phosphorelay pathway as a test case. In this way two paralogous type-A cytokinin Response Regulators were identified that are involved in root nodule symbiosis. MtRR9 and MtRR11 in Medicago truncatula, and an ortholog in Lotus japonicus, are rapidly induced upon rhizobium Nod factor signaling. Constitutive expression of MtRR9 results in arrested primordia that have emerged from cortical, endodermal and pericycle cells. In legumes lateral root primordia are not exclusively formed from pericycle cells, but also involves the root cortical cell layer. Therefore, the MtRR9 induced foci of cell divisions show a strong resemblance to lateral root primordia, suggesting an ancestral function of MtRR9 in this process. Together, these findings provide a proof of principle for the applied phylogenetic strategy to identify genes with a symbiotic function in legumes.
    Interfamily Transfer of Tomato Ve1 Mediates Verticillium Resistance in Arabidopsis
    Fradin, E.F. ; Abd-El-Haliem, A. ; Masini, L. ; Berg, G.C.M. van den; Joosten, M.H.A.J. ; Thomma, B.P.H.J. - \ 2011
    Plant Physiology 156 (2011)4. - ISSN 0032-0889 - p. 2255 - 2265.
    receptor-like proteins - leucine-rich repeat - disease resistance - cladosporium-fulvum - cell-death - recognitional specificity - scab resistance - innate immunity - plant-pathogen - gene family
    Vascular wilts caused by soil-borne fungal species of the Verticillium genus are devastating plant diseases. The most common species, Verticillium dahliae and Verticillium albo-atrum, have broad host ranges and are notoriously difficult to control. Therefore, genetic resistance is the preferred method for disease control. Only from tomato (Solanum lycopersicum) has a Verticillium resistance locus been cloned, comprising the Ve1 gene that encodes a receptor-like protein-type cell surface receptor. Due to lack of a suitable model for receptor-like protein (RLP)-mediated resistance signaling in Arabidopsis (Arabidopsis thaliana), so far relatively little is known about RLP signaling in pathogen resistance. Here, we show that Ve1 remains fully functional after interfamily transfer to Arabidopsis and that Ve1-transgenic Arabidopsis is resistant to race 1 but not to race 2 strains of V. dahliae and V. albo-atrum, nor to the Brassicaceae-specific pathogen Verticillium longisporum. Furthermore, we show that signaling components utilized by Ve1 in Arabidopsis to establish Verticillium resistance overlap with those required in tomato and include SERK3/BAK1, EDS1, and NDR1, which strongly suggests that critical components for resistance signaling are conserved. We subsequently investigated the requirement of SERK family members for Ve1 resistance in Arabidopsis, revealing that SERK1 is required in addition to SERK3/BAK1. Using virus-induced gene silencing, the requirement of SERK1 for Ve1-mediated resistance was confirmed in tomato. Moreover, we show the requirement of SERK1 for resistance against the foliar fungal pathogen Cladosporium fulvum mediated by the RLP Cf-4. Our results demonstrate that Arabidopsis can be used as model to unravel the genetics of Ve1-mediated resistance.
    A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots.
    Bishopp, A. ; Help, H. ; El-Showk, S. ; Weijers, D. ; Scheres, B.J.G. ; Friml, J. ; Benkova, E. ; Pekka Mahonen, A. ; Helariutta, Y. - \ 2011
    Current Biology 21 (2011)11. - ISSN 0960-9822 - p. 917 - 926.
    cup-shaped-cotyledon - stem-cell niche - class iiihd-zip - arabidopsis root - meristem activity - hormonal-control - gene family - embryo - efflux - embryogenesis
    Background Whereas the majority of animals develop toward a predetermined body plan, plants show iterative growth and continually produce new organs and structures from actively dividing meristems. This raises an intriguing question: How are these newly developed organs patterned? In Arabidopsis embryos, radial symmetry is broken by the bisymmetric specification of the cotyledons in the apical domain. Subsequently, this bisymmetry is propagated to the root promeristem. Results Here we present a mutually inhibitory feedback loop between auxin and cytokinin that sets distinct boundaries of hormonal output. Cytokinins promote the bisymmetric distribution of the PIN-FORMED (PIN) auxin efflux proteins, which channel auxin toward a central domain. High auxin promotes transcription of the cytokinin signaling inhibitor AHP6, which closes the interaction loop. This bisymmetric auxin response domain specifies the differentiation of protoxylem in a bisymmetric pattern. In embryonic roots, cytokinin is required to translate a bisymmetric auxin response in the cotyledons to a bisymmetric vascular pattern in the root promeristem. Conclusions Our results present an interactive feedback loop between hormonal signaling and transport by which small biases in hormonal input are propagated into distinct signaling domains to specify the vascular pattern in the root meristem. It is an intriguing possibility that such a mechanism could transform radial patterns and allow continuous vascular connections between other newly emerging organs.
    LysM-Type Mycorrhizal Receptor Recruited for Rhizobium Symbiosis in Nonlegume Parasponia
    Camp, R.H.M. Op den; Streng, A.J. ; Mita, S. De; Cao, Q. ; Polone, E. ; Liu, W. ; Ammiraju, J.S.S. ; Kudrna, D. ; Wing, R. ; Untergasser, A. ; Bisseling, T. ; Geurts, R. - \ 2011
    Science 331 (2011)6019. - ISSN 0036-8075 - p. 909 - 912.
    medicago-truncatula - gene family - nodulation - evolution - kinases - legume - endosymbiosis - bacteria - nodules - plants
    Rhizobium root nodule symbiosis is generally considered to be unique for legumes. However, there is one exception and that is Parasponia. In this nonlegume, the rhizobial nodule symbiosis evolved independently and is, like in legumes, induced by rhizobium Nod factors. We used Parasponia to identify genetic constrains underlying evolution of Nod factor signalling. Part of the signalling cascade, downstream of Nod factor perception, has been recruited from the more ancient arbuscular endomycorrhizal symbiosis. However, legume Nod factor receptors that activate this common signalling pathway are not essential for arbuscular endomycorrhizae. Here, we show that in Parasponia a single Nod factor-like receptor is indispensable for both symbiotic interactions. Therefore we conclude that also the Nod factor perception mechanism is recruited from the widespread endomycorrhizal symbiosis
    Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis
    Dalloul, R.A. ; Long, J.A. ; Zimin, A.V. ; Aslam, M.L. ; Crooijmans, R.P.M.A. ; Megens, H.J.W.C. ; Groenen, M. - \ 2010
    PloS Biology 8 (2010)9. - ISSN 1545-7885 - 21 p.
    high-throughput - monodelphis-domestica - molecular phylogeny - chicken genome - gene family - evolution - identification - diversity - birds - galliformes
    A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (~1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.
    Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire
    Lévesque, C.A. ; Brouwer, H. ; Cano, L. ; Hamilton, J.P. ; Holt, C. ; Huitema, E. ; Raffaele, S. ; Robideau, G.P. ; Thines, M. ; Win, J. ; Zerillo, M.M. ; Beakes, G.W. ; Boore, J.L. ; Busam, D. ; Dumas, B. ; Ferriera, S. ; Fuerstenberg, S.I. ; Gachon, C.M.M. ; Gaulin, E. ; Govers, F. ; Grenville-Briggs, L. ; Horner, N. ; Hostetler, J. ; Jiang, R.H.Y. ; Johnson, J. ; Krajaejun, T. ; Lin, H. ; Meijer, H.J.G. ; Moore, B. ; Morris, P. ; Phuntmart, V. ; Puiu, D. ; Shetty, J. ; Stajich, J.E. ; Tripathy, S. ; Wawra, S. ; West, P. van; Whitty, B.R. ; Coutinho, P.M. ; Henrissat, B. ; Martin, F. ; Thomas, P.D. ; Tyler, B.M. ; Vries, R.P. de; Kamoun, S. ; Yandell, M. ; Tisserat, N. ; Buell, C.R. - \ 2010
    Genome Biology 11 (2010)7. - ISSN 1474-7596 - 22 p.
    oomycete phytophthora-infestans - potato famine pathogen - protein families - mitochondrial genome - pleiotropic drug - gene family - arabidopsis-thaliana - cadherin superfamily - microbe interactions - molecular evolution
    Background - Pythium ultimum is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species. Results -The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related Phytophthora species, including the potato blight pathogen Phytophthora infestans. Whole transcriptome sequencing revealed expression of 86% of genes, with detectable differential expression of suites of genes under abiotic stress and in the presence of a host. The predicted proteome includes a large repertoire of proteins involved in plant pathogen interactions, although, surprisingly, the P. ultimum genome does not encode any classical RXLR effectors and relatively few Crinkler genes in comparison to related phytopathogenic oomycetes. A lower number of enzymes involved in carbohydrate metabolism were present compared to Phytophthora species, with the notable absence of cutinases, suggesting a significant difference in virulence mechanisms between P. ultimum and more host-specific oomycete species. Although we observed a high degree of orthology with Phytophthora genomes, there were novel features of the P. ultimum proteome, including an expansion of genes involved in proteolysis and genes unique to Pythium. We identified a small gene family of cadherins, proteins involved in cell adhesion, the first report of these in a genome outside the metazoans. Conclusions - Access to the P. ultimum genome has revealed not only core pathogenic mechanisms within the oomycetes but also lineage-specific genes associated with the alternative virulence and lifestyles found within the pythiaceous lineages compared to the Peronosporaceae.
    An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae (on linr)
    Wang, Kui-Lin ; Bolitho, Karen ; Grafton, Karryn ; Kortstee, A.J. ; Karunairetnam, Sakuntala ; McGhie, T.K. ; Espley, R.V. ; Hellens, R.P. ; Allan, A.C. - \ 2010
    BMC Plant Biology 10 (2010). - ISSN 1471-2229
    arabidopsis-thaliana - dna-binding - maize c1 - flavonoid biosynthesis - functional genomics - transgenic tobacco - red coloration - colorful model - dietary-intake - gene family
    Background - The control of plant anthocyanin accumulation is via transcriptional regulation of the genes encoding the biosynthetic enzymes. A key activator appears to be an R2R3 MYB transcription factor. In apple fruit, skin anthocyanin levels are controlled by a gene called MYBA or MYB1, while the gene determining fruit flesh and foliage anthocyanin has been termed MYB10. In order to further understand tissue-specific anthocyanin regulation we have isolated orthologous MYB genes from all the commercially important rosaceous species. Results - We use gene specific primers to show that the three MYB activators of apple anthocyanin (MYB10/MYB1/MYBA) are likely alleles of each other. MYB transcription factors, with high sequence identity to the apple gene were isolated from across the rosaceous family (e.g. apples, pears, plums, cherries, peaches, raspberries, rose, strawberry). Key identifying amino acid residues were found in both the DNA-binding and c-terminal domains of these MYBs. The expression of these MYB10 genes correlates with fruit and flower anthocyanin levels. Their function was tested in tobacco and strawberry. In tobacco, these MYBs were shown to induce the anthocyanin pathway when co-expressed with bHLHs, while over-expression of strawberry and apple genes in the crop of origin elevates anthocyanins. Conclusions - This family-wide study of rosaceous R2R3 MYBs provides insight into the evolution of this plant trait. It has implications for the development of new coloured fruit and flowers, as well as aiding the understanding of temporal-spatial colour change
    Arabidopsis L-type lectin receptor kinases: phylogeny, classification, and expression profiles
    Bouwmeester, K. ; Govers, F. - \ 2009
    Journal of Experimental Botany 60 (2009)15. - ISSN 0022-0957 - p. 4383 - 4396.
    protein-kinase - gene family - s-locus - extracellular domain - wall - thaliana - evolution - wak1 - identification - perception
    In plants, lectin receptor kinases are considered to play crucial roles during development and in the adaptive response to various stimuli. Arabidopsis lectin receptor kinases can be divided into three type-classes based on sequence similarity of their extracellular lectin motifs. The current study focuses on the legume-like lectin receptor kinases (LecRKs), which are regarded as ideal candidates for monitoring cell wall integrity and are possibly functional in adaptive responses. An inventory of the Arabidopsis LecRK gene family is presented here. It consists of 45 members including three that were recently identified; two encode N-terminal truncated variants one of which has two in tandem kinase domains. Phylogenetic trees derived from full-length amino acid sequence alignments were highly concordant to phylograms that were purely based on lectin motifs or kinase domains. The phylograms allowed reclassification of the LecRK genes and hence a new proposal for gene nomenclature was suggested. In addition, a comprehensive expression analysis was executed by exploring public repositories. This revealed that several LecRK genes are differentially expressed during plant growth and development. Moreover, multiple LecRKs appear to be induced upon treatment with elicitors and pathogen infection. Variation in gene expression was also analysed in seedlings of diverse Arabidopsis accessions. Taken together, this study provides a genome-wide overview of the LecRK gene family and an up-to-date classification using a novel and systematic gene nomenclature.
    Tetraploid and hexaploid wheat varieties reveal large differences in expression of alpha-gliadins from homoelogous Gli-loci
    Salentijn, E.M.J. ; Goryunova, S.V. ; Bas, N. ; Meer, I.M. van der; Broeck, H.C. van den; Bastien, T.A. ; Gilissen, L.J.W.J. ; Smulders, M.J.M. - \ 2009
    BMC Genomics 10 (2009). - ISSN 1471-2164 - p. 48 - 48.
    single-nucleotide polymorphisms - celiac-disease patients - t-cell epitope - gene family - dna pools - protein - gluten - pyrosequencing(tm) - diversity - genomes
    Background - A-gliadins form a multigene protein family encoded by multiple ¿-gliadin (Gli-2) genes at three genomic loci, Gli-A2, Gli-B2 and Gli-D2, respectively located on the homoeologous wheat chromosomes 6AS, 6BS, and 6DS. These proteins contain a number of important celiac disease (CD)-immunogenic domains. The ¿-gliadins expressed from the Gli-B2 locus harbour fewer conserved CD-epitopes than those from Gli-A2, whereas the Gli-D2 gliadins have the highest CD-immunogenic potential. In order to detect differences in the highly CD-immunogenic ¿-gliadin fraction we determined the relative expression level from the homoeologous Gli-2 loci in various tetraploid and hexaploid wheat genotypes by using a quantitative pyrosequencing method and by analyzing expressed sequence tag (EST) sequences. Results - We detected large differences in relative expression levels of ¿-gliadin genes from the three homoeologous loci among wheat genotypes, both as relative numbers of expressed sequence tag (EST) sequences from specific varieties and when using a quantitative pyrosequencing assay specific for Gli-A2 genes. The relative Gli-A2 expression level in a tetraploid durum wheat cultivar ('Probstdorfer Pandur') was 41%. In genotypes derived from landraces, the Gli-A2 frequency varied between 12% and 58%. In some advanced hexaploid bread wheat cultivars the genes from locus Gli-B2 were hardly expressed (e.g., less than 5% in 'Lavett') but in others they made up more than 40% (e.g., in 'Baldus'). Conclusion - Here, we have shown that large differences exist in relative expression levels of ¿-gliadins from the homoeologous Gli-2 loci among wheat genotypes. Since the homoelogous genes differ in the amount of conserved CD-epitopes, screening for differential expression from the homoeologous Gli-2 loci can be employed for the pre-selection of wheat varieties in the search for varieties with very low CD-immunogenic potential. Pyrosequencing is a method that can be employed for such a 'gene family-specific quantitative transcriptome profiling'
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