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functional characterization of proanthocyanidin pathway enzymes from tea and their application for metabolic engineering.tea (camellia sinensis) is rich in specialized metabolites, especially polyphenolic proanthocyanidins (pas) and their precursors. to better understand the pa pathway in tea, we generated a complementary dna library from leaf tissue of the blister blight-resistant tea cultivar tri2043 and functionally characterized key enzymes responsible for the biosynthesis of pa precursors. structural genes encoding enzymes involved in the general phenylpropanoid/flavonoid pathway and the pa-specific branch pa ...201323288883
growth and nodulation of symbiotic medicago truncatula at different levels of phosphorus availability.medicago truncatula is an important model plant for characterization of p deficiency on leguminous plants at the physiological and molecular levels. growth optimization of this plant with regard to p supply is the first essential step for elucidation of the role of p in regulation of nodulation. hence, a study was carried out to address the growth pattern of m. truncatula hydroponically grown at different gradual increases in p levels. the findings revealed that m. truncatula had a narrow p regi ...201323682114
a medicago truncatula abc transporter belonging to subfamily g modulates the level of isoflavonoids.full-sized atp-binding cassette (abc) transporters of the g subfamily (abcg) are considered to be essential components of the plant immune system. these proteins have been proposed to be implicated in the active transmembrane transport of various secondary metabolites. despite the importance of abcg-based transport for plant-microbe interactions, these proteins are still poorly recognized in legumes. the experiments described here demonstrated that the level of medicago truncatula abcg10 (mtabcg ...201323314816
single-plant, sterile microcosms for nodulation and growth of the legume plant medicago truncatula with the rhizobial symbiont sinorhizobium meliloti.rhizobial bacteria form symbiotic, nitrogen-fixing nodules on the roots of compatible host legume plants. one of the most well-developed model systems for studying these interactions is the plant medicago truncatula cv. jemalong a17 and the rhizobial bacterium sinorhizobium meliloti 1021. repeated imaging of plant roots and scoring of symbiotic phenotypes requires methods that are non-destructive to either plants or bacteria. the symbiotic phenotypes of some plant and bacterial mutants become ap ...201324121837
gene silencing in medicago truncatula roots using rnai.medicago truncatula is used widely as a model system for studies of root symbioses, interactions with parasitic nematodes and fungal pathogens, as well as studies of development and secondary metabolism. in medicago truncatula as well as other legumes, rna interference (rnai) coupled with agrobacterium rhizogenes-mediated root transformation, has been used very successfully for analyses of gene function in roots. one of the major advantages of this approach is the ease and relative speed with wh ...201323996315
trans-specific gene silencing of acetyl-coa carboxylase in a root-parasitic plant.parasitic species of the family orobanchaceae are devastating agricultural pests in many parts of the world. the control of weedy orobanchaceae spp. is challenging, particularly due to the highly coordinated life cycles of the parasite and host plants. although host genetic resistance often provides the foundation of plant pathogen management, few genes that confer resistance to root parasites have been identified and incorporated into crop species. members of the family orobanchaceae acquire wa ...201323383721
transient gene expression in medicago truncatula leaves via agroinfiltration.transient expression is a powerful method for the functional characterization of genes. in this chapter, we outline a protocol for the transient expression of constructs in medicago truncatula leaves using agrobacterium tumefaciens infiltration. using quantitative real-time pcr we demonstrate that the infiltration of a construct containing the legume anthocyanin production 1 (lap1) transcription factor results in the strong upregulation of key biosynthetic genes and the accumulation of anthocyan ...201323996318
stable transformation of medicago truncatula cv. jemalong for gene analysis using agrobacterium tumefaciens.medicago truncatula is a model legume that has all the genomic resources to be suitable as a model for functional genomics. transformation to produce transgenic plants is part of this toolkit, enabling a spectrum of approaches to study gene function: including knockdown, overexpression, reporter genes for gene expression, and proteins tagged with fluorescent proteins such as gfp. a special genetic line is necessary for transformation and jemalong 2ha derived from cv. jemalong is used in the meth ...201323996317
a tandem kunitz protease inhibitor (kpi106)-serine carboxypeptidase (scp1) controls mycorrhiza establishment and arbuscule development in medicago truncatula.plant proteases and protease inhibitors are involved in plant developmental processes including those involving interactions with microbes. here we show that a tandem between a kunitz protease inhibitor (kpi106) and a serine carboxypeptidase (scp1) controls arbuscular mycorrhiza development in the root cortex of medicago truncatula. both proteins are only induced during mycorrhiza formation and belong to large families whose members are also mycorrhiza-specific. furthermore, the interaction betw ...201323662629
evidence for participation of the methionine sulfoxide reductase repair system in plant seed longevity.seeds are in a natural oxidative context leading to protein oxidation. although inevitable for proper progression from maturation to germination, protein oxidation at high levels is detrimental and associated with seed aging. oxidation of methionine to methionine sulfoxide is a common form of damage observed during aging in all organisms. this damage is reversible through the action of methionine sulfoxide reductases (msrs), which play key roles in lifespan control in yeast and animal cells. to ...201323401556
combinatorial biosynthesis of legume natural and rare triterpenoids in engineered yeast.triterpenoid saponins are a diverse group of specialized (secondary) metabolites with many biological properties. the model legume medicago truncatula has an interesting profile of triterpenoid saponins from which sapogenins are differentiated into hemolytic and non-hemolytic types according to the position of their functional groups and hemolytic properties. gene co-expression analysis confirmed the presence of candidate p450s whose gene expression correlated highly with that of β-amyrin syntha ...201323378447
definition and evolution of a new symbiovar, sv. rigiduloides, among ensifer meliloti efficiently nodulating medicago species.understanding functional diversity is one of the main goals of microbial ecology, and definition of new bacterial ecotypes contributes significantly to this objective. nitrogen-fixing bacteria provide a good system for investigation of ecotypes/biovars/symbiovars, as they present different specific associations with several host plants. this specific symbiosis is reflected both in the nodulation and fixation efficiency and in genetic characters of the bacteria, and several biovars have already b ...201323871297
peribacteroid space acidification: a marker of mature bacteroid functioning in medicago truncatula nodules.legumes form a symbiotic interaction with rhizobiaceae bacteria, which differentiate into nitrogen-fixing bacteroids within nodules. here, we investigated in vivo the ph of the peribacteroid space (pbs) surrounding the bacteroid and ph variation throughout symbiosis. in vivo confocal microscopy investigations, using acidotropic probes, demonstrated the acidic state of the pbs. in planta analysis of nodule senescence induced by distinct biological processes drastically increased pbs ph in the n2 ...201323586685
the succinoglycan endoglycanase encoded by exok is required for efficient symbiosis of sinorhizobium meliloti 1021 with the host plants medicago truncatula and medicago sativa (alfalfa).the acidic polysaccharide succinoglycan produced by the nitrogen-fixing rhizobial symbiont sinorhizobium meliloti 1021 is required for this bacterium to invade the host plant medicago truncatula and to efficiently invade the host plant m. sativa (alfalfa). the β-glucanase enzyme encoded by exok has previously been demonstrated to cleave succinoglycan and participate in producing the low molecular weight form of this polysaccharide. here, we show that exok is required for efficient s. meliloti in ...201323656330
effects of rhizophagus irregularis mucl 41833 on the reproduction of radopholus similis in banana plantlets grown under in vitro culture conditions.the role of arbuscular mycorrhizal fungi (amf) in the control of migratory endoparasitic nematodes is nowadays largely admitted. most studies were conducted under greenhouse conditions and a few used in vitro cultures with transgenic root organs. here, we reported, for the first time, on the interaction between an amf, rhizophagus irregularis mucl 41833 and radopholus similis in roots of banana plantlets grown under in vitro culture conditions. the banana plantlets were pre-mycorrhized in an ext ...201323111398
mtqrrs1, an r-locus required for medicago truncatula quantitative resistance to ralstonia solanacearum.ralstonia solanacearum is a major soilborne pathogen that attacks > 200 plant species, including major crops. to characterize mtqrrs1, a major quantitative trait locus (qtl) for resistance towards this bacterium in the model legume medicago truncatula, genetic and functional approaches were combined. qtl analyses together with disease scoring of heterogeneous inbred families were used to define the locus. the candidate region was studied by physical mapping using a bacterial artificial chromosom ...201323638965
does phloem-based resistance to aphid feeding affect host-plant acceptance for reproduction? parturition of the pea aphid, acyrthosiphon pisum, on two near-isogenic lines of medicago truncatula.probing behaviour (prior to parturition) and parturition of two clones (ps01 and n116) of the pea aphid, acyrthosiphon pisum on two genotypes (near-isogenic lines (nils)) (q174_5.13 and q174_9.10) of medicago truncatula were investigated using electrical penetration graph (epg) coupled with simultaneous visual monitoring for parturition. line q174_5.13 has been reported to show a phloem-based resistance to feeding in the clone ps01 but to be susceptible to the clone n116, whereas q174_9.10 has s ...201323823797
pea aphid promotes amino acid metabolism both in medicago truncatula and bacteriocytes to favor aphid population growth under elevated co2.rising atmospheric co(2) levels can dilute the nitrogen (n) resource in plant tissue, which is disadvantageous to many herbivorous insects. aphids appear to be an exception that warrants further study. the effects of elevated co(2) (750 ppm vs. 390 ppm) were evaluated on n assimilation and transamination by two medicago truncatula genotypes, a n-fixing-deficient mutant (dnf1) and its wild-type control (jemalong), with and without pea aphid (acyrthosiphon pisum) infestation. elevated co(2) increa ...201323686968
medicago truncatula increases its iron-uptake mechanisms in response to volatile organic compounds produced by sinorhizobium meliloti.medicago truncatula represents a model plant species for understanding legume-bacteria interactions. m. truncatula roots form a specific root-nodule symbiosis with the nitrogen-fixing bacterium sinorhizobium meliloti. symbiotic nitrogen fixation generates high iron (fe) demands for bacterial nitrogenase holoenzyme and plant leghemoglobin proteins. leguminous plants acquire fe via "strategy i," which includes mechanisms such as rhizosphere acidification and enhanced ferric reductase activity. in ...201323564626
aphanomyces euteiches cell wall fractions containing novel glucan-chitosaccharides induce defense genes and nuclear calcium oscillations in the plant host medicago truncatula.n-acetylglucosamine-based saccharides (chitosaccharides) are components of microbial cell walls and act as molecular signals during host-microbe interactions. in the legume plant medicago truncatula, the perception of lipochitooligosaccharide signals produced by symbiotic rhizobia and arbuscular mycorrhizal fungi involves the nod factor perception (nfp) lysin motif receptor-like protein and leads to the activation of the so-called common symbiotic pathway. in rice and arabidopsis, lysin motif re ...201324086432
medicago truncatula esn1 defines a genetic locus involved in nodule senescence and symbiotic nitrogen fixation.symbiotic interaction between medicago truncatula and sinorhizobium meliloti results in the formation on the host roots of new organs, nodules, in which biological nitrogen fixation takes place. in infected cells, rhizobia enclosed in a plant-derived membrane, the symbiosome membrane, differentiate to nitrogen-fixing bacteroids. the symbiosome membrane serves as an interface for metabolite and signal exchanges between the host cells and endosymbionts. at some point during symbiosis, symbiosomes ...201323634841
hydrogen peroxide-regulated genes in the medicago truncatula-sinorhizobium meliloti symbiosis.reactive oxygen species (ros), particularly hydrogen peroxide (h(2)o(2)), play an important role in signalling in various cellular processes. the involvement of h(2)o(2) in the medicago truncatula-sinorhizobium meliloti symbiotic interaction raises questions about its effect on gene expression. a transcriptome analysis was performed on inoculated roots of m. truncatula in which ros production was inhibited with diphenylene iodonium (dpi). in total, 301 genes potentially regulated by ros content ...201323347006
medicago truncatula dnf2 is a pi-plc-xd-containing protein required for bacteroid persistence and prevention of nodule early senescence and defense-like reactions.medicago truncatula and sinorhizobium meliloti form a symbiotic association resulting in the formation of nitrogen-fixing nodules. nodule cells contain large numbers of bacteroids which are differentiated, nitrogen-fixing forms of the symbiotic bacteria. in the nodules, symbiotic plant cells home and maintain hundreds of viable bacteria. in order to better understand the molecular mechanism sustaining the phenomenon, we searched for new plant genes required for effective symbiosis. we used a com ...201323278348
selective recruitment of mrnas and mirnas to polyribosomes in response to rhizobia infection in medicago truncatula.translation of mrnas is a key regulatory step that contributes to the coordination and modulation of eukaryotic gene expression during development or adaptation to the environment. mrna stability or translatability can be regulated by the action of small regulatory rnas (srnas), which control diverse biological processes. under low nitrogen conditions, leguminous plants associate with soil bacteria and develop a new organ specialized in nitrogen fixation: the nodule. to gain insight into the tra ...201323050939
structural and functional studies of a phosphatidic acid-binding antifungal plant defensin mtdef4: identification of an rgfrrr motif governing fungal cell entry.mtdef4 is a 47-amino acid cysteine-rich evolutionary conserved defensin from a model legume medicago truncatula. it is an apoplast-localized plant defense protein that inhibits the growth of the ascomycetous fungal pathogen fusarium graminearum in vitro at micromolar concentrations. little is known about the mechanisms by which mtdef4 mediates its antifungal activity. in this study, we show that mtdef4 rapidly permeabilizes fungal plasma membrane and is internalized by the fungal cells where it ...201324324798
alternative splicing is required for rct1-mediated disease resistance in medicago truncatula.rct1 is a tir-nbs-lrr-type resistance (r) gene in medicago truncatula that confers resistance to multiple races of colletotrichum trifolii, a hemi-biotrophic fungal pathogen that causes anthracnose disease in medicago and other closely related legumes. rct1 undergoes alternative splicing at both coding and 3'-untranslated regions, thereby producing multiple transcript variants in its expression profile. alternative splicing of rct1 in the coding region results from the retention of intron 4. bec ...201323657790
nfp, a lysm protein controlling nod factor perception, also intervenes in medicago truncatula resistance to pathogens.plant lysm proteins control the perception of microbial-derived n-acetylglucosamine compounds for the establishment of symbiosis or activation of plant immunity. this raises questions about how plants, and notably legumes, can differentiate friends and foes using similar molecular actors and whether any receptors can intervene in both symbiosis and resistance. to study this question, nfp and lyk3 lysm-receptor like kinase mutants of medicago truncatula that are affected in the early steps of nod ...201323432463
high-quality draft genome sequence of xanthomonas alfalfae subsp. alfalfae strain cfbp 3836.we report the high-quality draft genome sequence of xanthomonas alfalfae subsp. alfalfae strain cfbp 3836, the causal agent of bacterial leaf and stem spot in lucerne (medicago sativa). comparative genomics will help to decipher the mechanisms provoking disease and triggering the defense responses of this pathogen of the model legume medicago truncatula.201324336373
failure of self-control: defense-like reactions during legume/rhizobia symbiosis.medicago truncatula and sinorhizobium meliloti form a symbiotic association resulting in the formation of nitrogen-fixing nodules. in this organ, symbiotic cells contain large numbers of bacteroids. remarkably, this chronic infection does not trigger visible defense reactions. despite the importance of this phenomenon for potential transfer of the symbiotic capacity to non-legume plants, the molecular mechanisms underlying this tolerance are not understood. we have characterized the dnf2 m. trun ...201323425859
short-chain chitin oligomers from arbuscular mycorrhizal fungi trigger nuclear ca2+ spiking in medicago truncatula roots and their production is enhanced by strigolactone.the primary objective of this study was to identify the molecular signals present in arbuscular mycorrhizal (am) germinated spore exudates (gses) responsible for activating nuclear ca(2+) spiking in the medicago truncatula root epidermis. medicago truncatula root organ cultures (rocs) expressing a nuclear-localized cameleon reporter were used as a bioassay to detect am-associated ca(2+) spiking responses and lc-ms to characterize targeted molecules in gses. this approach has revealed that short- ...201323384011
molecular cloning and characterization of a gene regulating flowering time from alfalfa (medicago sativa l.).genes that regulate flowering time play crucial roles in plant development and biomass formation. based on the cdna sequence of medicago truncatula (accession no. ay690425), the lfy gene of alfalfa was cloned. sequence similarity analysis revealed high homology with flo/lfy family genes of other plants. when fused to the green fluorescent protein, mslfy protein was localized in the nucleus of onion (allium cepa l.) epidermal cells. the rt-qpcr analysis of mslfy expression patterns showed that th ...201323670041
maldi mass spectrometry-assisted molecular imaging of metabolites during nitrogen fixation in the medicago truncatula-sinorhizobium meliloti symbiosis.symbiotic associations between leguminous plants and nitrogen-fixing rhizobia culminate in the formation of specialized organs called root nodules, in which the rhizobia fix atmospheric nitrogen and transfer it to the plant. efficient biological nitrogen fixation depends on metabolites produced by and exchanged between both partners. the medicago truncatula-sinorhizobium meliloti association is an excellent model for dissecting this nitrogen-fixing symbiosis because of the availability of geneti ...201323551619
the trans-acting short interfering rna3 pathway and no apical meristem antagonistically regulate leaf margin development and lateral organ separation, as revealed by analysis of an argonaute7/lobed leaflet1 mutant in medicago truncatula.leaf shape elaboration and organ separation are critical for plant morphogenesis. we characterized the developmental roles of lobed leaflet1 by analyzing a recessive mutant in the model legume medicago truncatula. an ortholog of arabidopsis thaliana argonaute7 (ago7), mt-ago7/lobed leaflet1, is required for the biogenesis of a trans-acting short interfering rna (ta-sirna) to negatively regulate the expression of auxin response factors in m. truncatula. loss of function in ago7 results in pleiotr ...201324368797
agamous-like15 promotes somatic embryogenesis in arabidopsis and soybean in part by the control of ethylene biosynthesis and response.many of the regulatory processes occurring during plant embryogenesis are still unknown. relatively few cells are involved, and they are embedded within maternal tissues, making this developmental phase difficult to study. somatic embryogenesis is a more accessible system, and many important regulatory genes appear to function similar to zygotic development, making somatic embryogenesis a valuable model for the study of zygotic processes. to better understand the role of the arabidopsis (arabido ...201323457229
conservation, divergence, and genome-wide distribution of pal and pox a gene families in plants.genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (pal) and peroxidase a (pox a) enzymes in nine plant species representing very diverse groups like legumes (glycine max and medicago truncatula), fruits (vitis vinifera), cereals (sorghum bicolor, zea mays, and oryza sativa), trees (populus trichocarpa), and model dicot (arabidopsis thaliana) and monocot (brachypodium distachyon) species. a total of 87 and ...201323671845
evaluation of genome sequencing quality in selected plant species using expressed sequence tags.with the completion of genome sequencing projects for more than 30 plant species, large volumes of genome sequences have been produced and stored in online databases. advancements in sequencing technologies have reduced the cost and time of whole genome sequencing enabling more and more plants to be subjected to genome sequencing. despite this, genome sequence qualities of multiple plants have not been evaluated.201323922843
isolation and functional characterization of a salt responsive transcriptional factor, lrbzip from lotus root (nelumbo nucifera gaertn).basic leucine zipper transcription factor (bzip) is involved in signaling transduction for various stress responses. here we reported a bzip transcription factor (accession: jx887153) isolated from a salt-resistant lotus root using cdna-aflp approach with rt-pcr and race-pcr method. full-length cdna which consisted of a single open reading frame encoded a putative polypeptide of 488 amino acids. on the basis of 78, 76, and 75 % sequence similarity with the bzips from medicago truncatula (xp_0035 ...201323288562
structural and functional characterization of annexin 1 from medicago truncatula.annexins are calcium- and membrane-binding proteins that have been shown to have diverse properties such as actin, integrin and gtp binding, both in animals and plants. recently, medicago truncatula annexin 1 (annmt1) has been suggested to participate in nodulation (nod factor signaling) and mycorrhization in legume plants. in this report we demonstrate for the first time that recombinant annmt1 (rec-annmt1) mediates membrane permeabilization to cations with conductance ranging from 16 ps to 329 ...201324056127
medicago glucosyltransferase ugt72l1: potential roles in proanthocyanidin biosynthesis.in the first reaction specific for proanthocyanidin (pa) biosynthesis in arabidopsis thaliana and medicago truncatula, anthocyanidin reductase (anr) converts cyanidin to (-)-epicatechin. the glucosyltransferase ugt72l1 catalyzes formation of epicatechin 3'-o-glucoside (e3'og), the preferred substrate for mate transporters implicated in pa biosynthesis in both species. the mechanism of pa polymerization is still unclear, but may involve the laccase-like polyphenol oxidase transparent testa 10 (tt ...201323592226
iron deficiency in plants: an insight from proteomic approaches.iron (fe) deficiency chlorosis is a major nutritional disorder for crops growing in calcareous soils, and causes decreases in vegetative growth as well as marked yield and quality losses. with the advances in mass spectrometry techniques, a substantial body of knowledge has arisen on the changes in the protein profiles of different plant parts and compartments as a result of fe deficiency. changes in the protein profile of thylakoids from several species have been investigated using gel-based tw ...201323898336
mutually exclusive alterations in secondary metabolism are critical for the uptake of insoluble iron compounds by arabidopsis and medicago truncatula.the generally low bioavailability of iron in aerobic soil systems forced plants to evolve sophisticated genetic strategies to improve the acquisition of iron from sparingly soluble and immobile iron pools. to distinguish between conserved and species-dependent components of such strategies, we analyzed iron deficiency-induced changes in the transcriptome of two model species, arabidopsis (arabidopsis thaliana) and medicago truncatula. transcriptional profiling by rna sequencing revealed a massiv ...201323735511
systems biology-based approaches toward understanding drought tolerance in food crops.economically important crops, such as maize, wheat, rice, barley, and other food crops are affected by even small changes in water potential at important growth stages. developing a comprehensive understanding of host response to drought requires a global view of the complex mechanisms involved. research on drought tolerance has generally been conducted using discipline-specific approaches. however, plant stress response is complex and interlinked to a point where discipline-specific approaches ...201322364373
detecting small plant peptides using spada (small peptide alignment discovery application).small peptides encoded as one- or two-exon genes in plants have recently been shown to affect multiple aspects of plant development, reproduction and defense responses. however, popular similarity search tools and gene prediction techniques generally fail to identify most members belonging to this class of genes. this is largely due to the high sequence divergence among family members and the limited availability of experimentally verified small peptides to use as training sets for homology sear ...201324256031
integrated consensus map of cultivated peanut and wild relatives reveals structures of the a and b genomes of arachis and divergence of the legume genomes.the complex, tetraploid genome structure of peanut (arachis hypogaea) has obstructed advances in genetics and genomics in the species. the aim of this study is to understand the genome structure of arachis by developing a high-density integrated consensus map. three recombinant inbred line populations derived from crosses between the a genome diploid species, arachis duranensis and arachis stenosperma; the b genome diploid species, arachis ipaënsis and arachis magna; and between the ab genome te ...201323315685
mitochondrial genome sequence of the legume vicia faba.the number of plant mitochondrial genomes sequenced exceeds two dozen. however, for a detailed comparative study of different phylogenetic branches more plant mitochondrial genomes should be sequenced. this article presents sequencing data and comparative analysis of mitochondrial dna (mtdna) of the legume vicia faba. the size of the v. faba circular mitochondrial master chromosome of cultivar broad windsor was estimated as 588,000 bp with a genome complexity of 387,745 bp and 52 conservative mi ...201323675376
comparative transcriptional profiling provides insights into the evolution and development of the zygomorphic flower of vicia sativa (papilionoideae).vicia sativa (the common vetch) possesses a predominant zygomorphic flower and belongs to the subfamily papilionoideae, which is related to arabidopsis thaliana in the eurosid ii clade of the core eudicots. each vetch flower consists of 21 concentrically arranged organs: the outermost five sepals, then five petals and ten stamens, and a single carpel in the center.201323437373
an experimental system to study responses of medicago truncatula roots to chitin oligomers of high degree of polymerization and other microbial elicitors.a fully acetylated, soluble co preparation of mean dp of ca. 7 was perceived with high sensitivity by m. truncatula in a newly designed versatile root elicitation assay. the root system of legume plants interacts with a large variety of microorganisms, either pathogenic or symbiotic. understanding how legumes recognize and respond specifically to pathogen-associated or symbiotic signals requires the development of standardized bioassays using well-defined preparations of the corresponding signal ...201323314495
plantrna, a database for trnas of photosynthetic eukaryotes.plantrna database (http://plantrna.ibmp.cnrs.fr/) compiles transfer rna (trna) gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. the set of annotated trna gene sequences has been manually curated for maximum quality and confidence. the novelty of this database resides in the inclusion of biological information relevant to the function of all the trnas entered in the library. this includes 5'- and 3'-flanking sequences, a and b box sequences, regio ...201323066098
the phytochrome gene family in soybean and a dominant negative effect of a soybean phya transgene on endogenous arabidopsis phya.the evolutionary origin of the phytochrome genes in soybean was analyzed. the expression profiles of phya paralogs were characterized. the heterologous expression of gmphya1 in arabidopsis resulted in longer hypocotyls. the phytochromes (phy) are a small family of red/far-red light photoreceptors which regulate a number of important developmental responses in plants. so far, the members of the phy gene family in soybean (glycine max) remain unclear and an understanding of each member's physiolog ...201324013793
the model legume genomes.the primary model legumes to date have been medicago truncatula and lotus japonicus. both species are tractable both genetically and in the greenhouse, and for both, substantial sets of tools and resources for molecular genetic research have been assembled. as sequencing costs have declined, however, additional legume genomes have been sequenced, and the funding available to crops such as soybean has enabled these to be developed to the status of genetic models in their own right. this chapter, ...201323996304
legumegrn: a gene regulatory network prediction server for functional and comparative studies.building accurate gene regulatory networks (grns) from high-throughput gene expression data is a long-standing challenge. however, with the emergence of new algorithms combined with the increase of transcriptomic data availability, it is now reachable. to help biologists to investigate gene regulatory relationships, we developed a web-based computational service to build, analyze and visualize grns that govern various biological processes. the web server is preloaded with all available affymetri ...201323844010
impact of whole-genome and tandem duplications in the expansion and functional diversification of the f-box family in legumes (fabaceae).f-box proteins constitute a large gene family that regulates processes from hormone signaling to stress response. f-box proteins are the substrate recognition modules of scf e3 ubiquitin ligases. here we report very distinct trends in family size, duplication, synteny and transcription of f-box genes in two nitrogen-fixing legumes, glycine max (soybean) and medicago truncatula (alfafa). while the soybean fbx genes emerged mainly through segmental duplications (including whole-genome duplications ...201323390519
evolutionary history of mitogen-activated protein kinase (mapk) genes in lotus, medicago, and phaseolus.mitogen-activated protein kinase (mapk) genes encode proteins that mediate various signaling pathways associated with biotic and abiotic stress responses in eukaryotes. the mapk genes form a 3-tier signal transduction cascade between cellular stimuli and physiological responses. recent identification of soybean mapks and availability of genome sequences from other legume species allowed us to identify their mapk genes. the main objectives of this study were to identify mapks in 3 legume species, ...201324317362
[molecular evolution of orf1 gene in plant ltr-retrotransposons].ltr-retrotransposons are the major dna components in plant genomes. they usually contain gag and pol, two genes necessary for transpositinal process. our previous study on soybean genome annotation identified a sare ltr-retrotransposon family, which carries the third gene, orf1. using a bioinformatics approach, we here reported that 7 out of 33 sequenced genomes have some ltr-retrotransposons with an extra orf1 gene/gene fragment (approximately 1-2 kb) in the region between 5' ltr and gag gene, ...201324400486
comparative sequence analysis of nitrogen fixation-related genes in six legumes.legumes play an important role as food and forage crops in international agriculture especially in developing countries. legumes have a unique biological process called nitrogen fixation (nf) by which they convert atmospheric nitrogen to ammonia. although legume genomes have undergone polyploidization, duplication and divergence, nf-related genes, because of their essential functional role for legumes, might have remained conserved. to understand the relationship of divergence and evolutionary p ...201323986765
snp marker discovery, linkage map construction and identification of qtls for enhanced salinity tolerance in field pea (pisum sativum l.).field pea (pisum sativum l.) is a self-pollinating, diploid, cool-season food legume. crop production is constrained by multiple biotic and abiotic stress factors, including salinity, that cause reduced growth and yield. recent advances in genomics have permitted the development of low-cost high-throughput genotyping systems, allowing the construction of saturated genetic linkage maps for identification of quantitative trait loci (qtls) associated with traits of interest. genetic markers in clos ...201324134188
insights into the insect salivary gland proteome: diet-associated changes in caterpillar labial salivary proteins.the primary function of salivary glands is fluid and protein secretion during feeding. compared to mammalian systems, little is known about salivary protein secretion processes and the effect of diet on the salivary proteome in insect models. therefore, the effect of diet nutritional quality on caterpillar labial salivary gland proteins was investigated using an unbiased global proteomic approach by nanolc/esi/tandem ms. caterpillars of the beet armyworm, spodoptera exigua hübner, were fed one o ...201323353727
spectroscopic determination of the toxicity, absorption, reduction, and translocation of cr(vi) in two magnoliopsida species.hexavalent chromium is a contaminant highly mobile in the environment that is toxic for plants at low concentrations. in this work, the physiological response of convolvulus arvensis and medicago truncatula plants to cr(vi) treatments was compared. c. arvensis is a potential cr hyperaccumulator well adapted to semiarid conditions that biotransform cr(vi) to the less toxic cr(iii). m. truncatula is a model plant well adapted to semiarid conditions with a well studied genetic response to heavy met ...201323487994
novel receptor-like kinases in cacao contain pr-1 extracellular domains.members of the pathogenesis-related protein 1 (pr-1) family are well-known markers of plant defence responses, forming part of the arsenal of the secreted proteins produced on pathogen recognition. here, we report the identification of two cacao (theobroma cacao l.) pr-1s that are fused to transmembrane regions and serine/threonine kinase domains, in a manner characteristic of receptor-like kinases (rlks). these proteins (tcpr-1f and tcpr-1g) were named pr-1 receptor kinases (pr-1rks). phylogene ...201323573899
transcriptional responses to drought stress in root and leaf of chickpea seedling.chickpea (cicer arietinum l.) is an important pulse crop grown mainly in the arid and semi-arid regions of the world. due to its taxonomic proximity with the model legume medicago truncatula and its ability to grow in arid soil, chickpea has its unique advantage to understand how plant responds to drought stress. in this study, an oligonucleotide microarray was used for analyzing the transcriptomic profiles of unigenes in leaf and root of chickpea seedling under drought stress, respectively. mic ...201222562393
characterization and genetic analysis of an ein4-like sequence (caetr-1) located in qtl(ar1) implicated in ascochyta blight resistance in chickpea.two alleles of a chickpea (cicer arietinum l.) ethylene receptor-like sequence (caetr-1) were sequence-characterized using synteny analysis with genome sequences of medicago truncatula l. the full length of the sequence obtained in the accession flip84-92c resistant to ascochyta blight (caetr-1a) span 4,428 bp, including the polyadenylation signal in the 3'-untranslated region (utr), whereas it has a 730 bp deletion in the 3'-utr region in the susceptible accession pi359075 (caetr-1b). the deduc ...201222238063
large-scale development of cost-effective snp marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes.a set of 2486 single nucleotide polymorphisms (snps) were compiled in chickpea using four approaches, namely (i) solexa/illumina sequencing (1409), (ii) amplicon sequencing of tentative orthologous genes (togs) (604), (iii) mining of expressed sequence tags (ests) (286) and (iv) sequencing of candidate genes (187). conversion of these snps to the cost-effective and flexible throughput competitive allele specific pcr (kaspar) assays generated successful assays for 2005 snps. these marker assays h ...201222703242
legumeip: an integrative database for comparative genomics and transcriptomics of model legumes.legumes play a vital role in maintaining the nitrogen cycle of the biosphere. they conduct symbiotic nitrogen fixation through endosymbiotic relationships with bacteria in root nodules. however, this and other characteristics of legumes, including mycorrhization, compound leaf development and profuse secondary metabolism, are absent in the typical model plant arabidopsis thaliana. we present legumeip (http://plantgrn.noble.org/legumeip/), an integrative database for comparative genomics and tran ...201222110036
large-scale development of cost-effective single-nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes.single-nucleotide polymorphisms (snps, >2000) were discovered by using rna-seq and allele-specific sequencing approaches in pigeonpea (cajanus cajan). for making the snp genotyping cost-effective, successful competitive allele-specific polymerase chain reaction (kaspar) assays were developed for 1616 snps and referred to as pkams (pigeonpea kaspar assay markers). screening of pkams on 24 genotypes [23 from cultivated species and 1 wild species (cajanus scarabaeoides)] defined a set of 1154 polym ...201223103470
leaf morphology in cowpea [vigna unguiculata (l.) walp]: qtl analysis, physical mapping and identifying a candidate gene using synteny with model legume species.cowpea [vigna unguiculata (l.) walp] exhibits a considerable variation in leaf shape. although cowpea is mostly utilized as a dry grain and animal fodder crop, cowpea leaves are also used as a high-protein pot herb in many countries of africa.201222691139
genome-enabled insights into legume biology.legumes are the third-largest family of angiosperms, the second-most-important crop family, and a key source of biological nitrogen in agriculture. recently, the genome sequences of glycine max (soybean), medicago truncatula, and lotus japonicus were substantially completed. comparisons among legume genomes reveal a key role for duplication, especially a whole-genome duplication event approximately 58 mya that is shared by most agriculturally important legumes. a second and more recent genome du ...201222404476
texture of cellulose microfibrils of root hair cell walls of arabidopsis thaliana, medicago truncatula, and vicia sativa.cellulose is the most abundant biopolymer on earth, and has qualities that make it suitable for biofuel. there are new tools for the visualisation of the cellulose synthase complexes in living cells, but those do not show their product, the cellulose microfibrils (cmfs). in this study we report the characteristics of cell wall textures, i.e. the architectures of the cmfs in the wall, of root hairs of arabidopsis thaliana, medicago truncatula and vicia sativa and compare the different techniques ...201222458271
identification and expression analysis of multiple fro gene copies in medicago truncatula.iron (fe) is an essential element for plant growth. commonly, this element is found in an oxidized form in soil, which is poorly available for plants. therefore, plants have evolved ferric-chelate reductase enzymes (fro) to reduce iron into a more soluble ferrous form. fe scarcity in plants induce the fro enzyme activity. although the legume medicago truncatula has been employed as a model for fro activity studies, only one copy of the m. truncatula mtfro1 gene has been characterized so far. in ...201223096909
boosting the globalization of plant proteomics through inppo: current developments and future prospects.the international plant proteomics organization (inppo) is a non-profit-organization consisting of people who are involved or interested in plant proteomics. inppo is constantly growing in volume and activity, which is mostly due to the realization among plant proteomics researchers worldwide for the need of such a global platform. their active participation resulted in the rapid growth within the first year of inppo's official launch in 2011 via its website (www.inppo.com) and publication of th ...201222290804
in silico identification of known osmotic stress responsive genes from arabidopsis in soybean and medicago.plants experience various environmental stresses, but tolerance to these adverse conditions is a very complex phenomenon. the present research aimed to evaluate a set of genes involved in osmotic response, comparing soybean and medicago with the well-described arabidopsis thaliana model plant. based on 103 arabidopsis proteins from 27 categories of osmotic stress response, comparative analyses against genosoja and medicago truncatula databases allowed the identification of 1,088 soybean and 1,21 ...201222802716
overall picture of expressed heat shock factors in glycine max, lotus japonicus and medicago truncatula.heat shock (hs) leads to the activation of molecular mechanisms, known as hs-response, that prevent damage and enhance survival under stress. plants have a flexible and specialized network of heat shock factors (hsfs), which are transcription factors that induce the expression of heat shock proteins. the present work aimed to identify and characterize the glycine max hsf repertory in the soybean genome project (genosoja platform), comparing them with other legumes (medicago truncatula and lotus ...201222802710
[expression analysis of the medicago truncatula floral specific expression genes].the expression of genes specific to floral organ is important for the floral organ formation and development in medicago truncatula. screening of the genes specifically expressed in m. truncatula flowers and comparing the expression patterns of their orthologous homologous genes among different model plants can provide novel insights into the functions of these genes in controlling the floral organ development in m. truncatula. according to the expression profile data of pistillata (pi), we scre ...201222659435
transcriptome sequencing of field pea and faba bean for discovery and validation of ssr genetic markers.field pea (pisum sativum l.) and faba bean (vicia faba l.) are cool-season grain legume species that provide rich sources of food for humans and fodder for livestock. to date, both species have been relative 'genomic orphans' due to limited availability of genetic and genomic information. a significant enrichment of genomic resources is consequently required in order to understand the genetic architecture of important agronomic traits, and to support germplasm enhancement, genetic diversity, pop ...201222433453
identification and characterization of resistance to cowpea aphid (aphis craccivora koch) in medicago truncatula.cowpea aphid (cpa; aphis craccivora) is the most important insect pest of cowpea and also causes significant yield losses in other legume crops including alfalfa, beans, chickpea, lentils, lupins and peanuts. in many of these crops there is no natural genetic resistance to this sap-sucking insect or resistance genes have been overcome by newly emerged cpa biotypes.201222759788
sulfenylated proteins in the medicago truncatula-sinorhizobium meliloti symbiosis.reactive oxygen species such as hydrogen peroxide (h(2)o(2)), play a crucial role as signaling molecules in the establishment and functioning of the nitrogen-fixing legume-rhizobium symbiosis. the regulation of protein function through oxidative modification has emerged as an important molecular mechanism modulating various biological processes. protein cysteine residues are known to be sensitive targets of h(2)o(2), in a posttranslational modification called sulfenylation. we trapped and identi ...201222634402
loss of abaxial leaf epicuticular wax in medicago truncatula irg1/palm1 mutants results in reduced spore differentiation of anthracnose and nonhost rust pathogens.to identify genes that confer nonhost resistance to biotrophic fungal pathogens, we did a forward-genetics screen using medicago truncatula tnt1 retrotransposon insertion lines. from this screen, we identified an inhibitor of rust germ tube differentation1 (irg1) mutant that failed to promote preinfection structure differentiation of two rust pathogens, phakopsora pachyrhizi and puccinia emaculata, and one anthracnose pathogen, colletotrichum trifolii, on the abaxial leaf surface. cytological an ...201222294617
subcellular targeting of an evolutionarily conserved plant defensin mtdef4.2 determines the outcome of plant-pathogen interaction in transgenic arabidopsis.the medicago truncatula gene encoding an evolutionarily conserved antifungal defensin mtdef4.2 was cloned and characterized. in silico expression analysis indicated that mtdef4.2 is expressed in many tissues during the normal growth and development of m. truncatula. mtdef4.2 exhibits potent broad-spectrum antifungal activity against various fusarium spp. transgenic arabidopsis thaliana lines in which mtdef4.2 was targeted to three different subcellular compartments were generated. these lines we ...201222776629
development of high-throughput snp-based genotyping in acacia auriculiformis x a. mangium hybrids using short-read transcriptome data.next generation sequencing has provided comprehensive, affordable and high-throughput dna sequences for single nucleotide polymorphism (snp) discovery in acacia auriculiformis and acacia mangium. like other non-model species, snp detection and genotyping in acacia are challenging due to lack of genome sequences. the main objective of this study is to develop the first high-throughput snp genotyping assay for linkage map construction of a. auriculiformis x a. mangium hybrids.201223265623
nitric oxide (no): a key player in the senescence of medicago truncatula root nodules.nitric oxide (no) is a signalling and defence molecule involved in diverse plant developmental processes, as well as in the plant response to pathogens. no has also been detected at different steps of the symbiosis between legumes and rhizobia. no is required for an optimal establishment of the medicago truncatula-sinorhizobium meliloti symbiotic interaction, but little is known about the role of no in mature nodules. here, we investigate the role of no in the late steps of symbiosis. genetic an ...201222937888
transcriptomic insights into mechanisms of symbiotic cooperation.intraspecific genetic variation can affect community structure and ecosystem processes (bolnick et al. 2011). it can also influence phenotypic expression by genotypes within other species to produce genotype-by-genotype (g × g) interaction (falconer & mackay 1996). evolution of one species drives correlated evolution of others when it causes g × g for fitness (thompson 2005). however, the mechanisms by which species interact also influence evolutionary outcomes (kummel & salant 2006; golubski & ...201223009647
repeated leaf wounding alters the colonization of medicago truncatula roots by beneficial and pathogenic microorganisms.in nature, plants are subject to various stresses that are often accompanied by wounding of the aboveground tissues. as wounding affects plants locally and systemically, we investigated the impact of leaf wounding on interactions of medicago truncatula with root-colonizing microorganisms, such as the arbuscular mycorrhizal (am) fungus glomus intraradices, the pathogenic oomycete aphanomyces euteiches and the nitrogen-fixing bacterium sinorhizobium meliloti. to obtain a long-lasting wound respons ...201222329418
overexpression of mtcas31 enhances drought tolerance in transgenic arabidopsis by reducing stomatal density.• dehydrins are a type of late embryogenesis abundant protein. some dehydrins are involved in the response to various abiotic stresses. accumulation of dehydrins enhances the drought, cold and salt tolerances of transgenic plants, although the underlying mechanism is unclear. mtcas31 (medicago truncatula cold-acclimation specific protein 31) is a y(2)k(4)-type dehydrin that was isolated from medicago truncatula. • we analyzed the subcellular and histochemical localization of mtcas31, and the exp ...201222510066
the medicago truncatula sucrose transporter family: characterization and implication of key members in carbon partitioning towards arbuscular mycorrhizal fungi.we identified de novo sucrose transporter (sut) genes involved in long-distance transport of sucrose from photosynthetic source leaves towards sink organs in the model leguminous species medicago truncatula. the identification and functional analysis of sugar transporters provide key information on mechanisms that underlie carbon partitioning in plant-microorganism interactions. in that way, full-length sequences of the m. truncatula sut (mtsut) family were retrieved and biochemical characteriza ...201222930732
putative use of a bacillus subtilis l194 strain for biocontrol of phoma medicaginis in medicago truncatula seedlings.an antagonist l194 strain against phoma medicaginis pathogenic fungi was isolated from tunisian soil (vicinity of tunis) and identified as bacillus subtilis based on biochemical characteristics and partial 16s rdna sequence. when cells were grown in a minimal medium for 24 h, spore culture supernatant exhibited 2-fold higher antifungal activity than vegetative cells. maldi-tof mass spectrometry analysis showed that l194 spores produced mainly iturins, surfactins and fengycins with long-chain fat ...201222579659
aeschynomene evenia, a model plant for studying the molecular genetics of the nod-independent rhizobium-legume symbiosis.research on the nitrogen-fixing symbiosis has been focused, thus far, on two model legumes, medicago truncatula and lotus japonicus, which use a sophisticated infection process involving infection thread formation. however, in 25% of the legumes, the bacterial entry occurs more simply in an intercellular fashion. among them, some aeschynomene spp. are nodulated by photosynthetic bradyrhizobium spp. that do not produce nod factors. this interaction is believed to represent a living testimony of t ...201222475377
simple and efficient methods to generate split roots and grafted plants useful for long-distance signaling studies in medicago truncatula and other small plants. 201222971438
rj (rj) genes involved in nitrogen-fixing root nodule formation in soybean.it has long been known that formation of symbiotic root nodules in soybean (glycine max (l.) merr.) is controlled by several host genes referred to as rj (rj) genes, but molecular cloning of these genes has been hampered by soybean's complicated genome structure and large genome size. progress in molecular identification of legume genes involved in root nodule symbiosis have been mostly achieved by using two model legumes, lotus japonicus and medicago truncatula, that have relatively simple and ...201223136493
high toxicity and specificity of the saponin 3-glca-28-ararhaxyl-medicagenate, from medicago truncatula seeds, for sitophilus oryzae.because of the increasingly concern of consumers and public policy about problems for environment and for public health due to chemical pesticides, the search for molecules more safe is currently of great importance. particularly, plants are able to fight the pathogens as insects, bacteria or fungi; so that plants could represent a valuable source of new molecules.201222536832
a medicago truncatula tobacco retrotransposon insertion mutant collection with defects in nodule development and symbiotic nitrogen fixation.a tnt1-insertion mutant population of medicago truncatula ecotype r108 was screened for defects in nodulation and symbiotic nitrogen fixation. primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (nod-), 51 mutants with totally i ...201222679222
transcriptional responses toward diffusible signals from symbiotic microbes reveal mtnfp- and mtdmi3-dependent reprogramming of host gene expression by arbuscular mycorrhizal fungal lipochitooligosaccharides.the formation of root nodules and arbuscular mycorrhizal (am) roots is controlled by a common signaling pathway including the calcium/calmodulin-dependent kinase doesn't make infection3 (dmi3). while nodule initiation by lipochitooligosaccharide (lco) nod factors is well characterized, diffusible am fungal signals were only recently identified as sulfated and nonsulfated lcos. irrespective of different outcomes, the perception of symbiotic lcos in medicago truncatula is mediated by the lysm rece ...201222652128
"ménage à trois": the presence/absence of thyme shapes the mutualistic interaction between the host plant medicago truncatula (fabaceae) and its symbiotic bacterium sinorhizobium meliloti.the long-term maintenance of specialized mutualisms remains an evolutionary puzzle. recent focus has been on factors governing the stability of these mutualisms, including sanctions by the host, partner choice, and coevolutionary constraint, that is, the genetic correlation (r(g)) between fitness of both partners. so far these studies have been typically carried out in a single environment. here, we ask if the genetic correlation between fitness of the host plant medicago truncatula (fabaceae) a ...201222957171
identification of distinct quantitative trait loci associated with defence against the closely related aphids acyrthosiphon pisum and a. kondoi in medicago truncatula.aphids are a major family of plant insect pests. medicago truncatula and acyrthosiphon pisum (pea aphid, pa) are model species with a suite of resources available to help dissect the mechanism underlying plant-aphid interactions. a previous study focused on monogenic and relatively strong resistance in m. truncatula to pa and other aphid species. in this study a moderate resistance to pa was characterized in detail in the m. truncatula line a17 and compared with the highly susceptible line a20 a ...201222442407
morphological and genetic changes induced by excess zn in roots of medicago truncatula a17 and a zn accumulating mutant.nutrient fluxes associated with legume-rhizobia symbioses are poorly understood and little is known regarding the influence of abiotic stresses on development and maintenance of n-fixing nodules and root system architecture (rsa). we examined effects of zn on nodule development and structure, root architecture, and expression of nodulation-related mirnas in medicago truncatula and the mutant, raz (requires additional zn).201223191938
is n-feedback involved in the inhibition of nitrogen fixation in drought-stressed medicago truncatula?drought stress is a major factor limiting nitrogen fixation (nf) in crop production. however, the regulatory mechanism involved and the origin of the inhibition, whether local or systemic, is still controversial and so far scarcely studied in temperate forage legumes. medicago truncatula plants were symbiotically grown with a split-root system and exposed to gradual water deprivation. physiological parameters, nf activity, and amino acid content were measured. the partial drought treatment inhib ...201223175536
expression dynamics of the medicago truncatula transcriptome during the symbiotic interaction with sinorhizobium meliloti: which role for nitric oxide?medicago truncatula is one of the most studied model plants. nevertheless, the genome of this legume remains incompletely determined. we used rna-seq to characterize the transcriptome during the early organogenesis of the nodule and during its functioning. we detected 37,333 expressed transcription units; to our knowledge, 1,670 had never been described before and were functionally annotated. we identified 7,595 new transcribed regions, mostly corresponding to 5' and 3' untranslated region exten ...201223136381
mapping the genetic basis of symbiotic variation in legume-rhizobium interactions in medicago truncatula.mutualisms are known to be genetically variable, where the genotypes differ in the fitness benefits they gain from the interaction. to date, little is known about the loci that underlie such genetic variation in fitness or whether the loci influencing fitness are partner specific, and depend on the genotype of the interaction partner. in the legume-rhizobium mutualism, one set of potential candidate genes that may influence the fitness benefits of the symbiosis are the plant genes involved in th ...201223173081
increased production of the exopolysaccharide succinoglycan enhances sinorhizobium meliloti 1021 symbiosis with the host plant medicago truncatula.the nitrogen-fixing rhizobial symbiont sinorhizobium meliloti 1021 produces acidic symbiotic exopolysaccharides that enable it to initiate and maintain infection thread formation on host legume plants. the exopolysaccharide that is most efficient in mediating this process is succinoglycan (exopolysaccharide i [epsi]), a polysaccharide composed of octasaccharide repeating units of 1 galactose and 7 glucose residues, modified with succinyl, acetyl, and pyruvyl substituents. previous studies had sh ...201222685282
a proteogenomic survey of the medicago truncatula genome.peptide sequencing by computational assignment of tandem mass spectra to a database of putative protein sequences provides an independent approach to confirming or refuting protein predictions based on large-scale dna and rna sequencing efforts. this use of mass spectrometrically-derived sequence data for testing and refining predicted gene models has been termed proteogenomics. we report herein the application of proteogenomic methodology to a database of 10.9 million tandem mass spectra collec ...201222774004
how to hierarchize the main physiological processes responsible for phenotypic differences in large-scale screening studies?one difficulty when analyzing the determinants at the origin of plant phenotypic differences is that measured plant traits are frequently integrative: they result from the integration of a large number of physiological processes under the control of genetic and environmental factors. in a previous report, we demonstrated that dissecting integrative traits into simpler components using a simple crop physiology model was a valuable method for detecting quantitative trait loci (qtl) related to the ...201222499204
(homo)glutathione deficiency impairs root-knot nematode development in medicago truncatula.root-knot nematodes (rkn) are obligatory plant parasitic worms that establish and maintain an intimate relationship with their host plants. during a compatible interaction, rkn induce the redifferentiation of root cells into multinucleate and hypertrophied giant cells essential for nematode growth and reproduction. these metabolically active feeding cells constitute the exclusive source of nutrients for the nematode. detailed analysis of glutathione (gsh) and homoglutathione (hgsh) metabolism de ...201222241996
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