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large-scale transcriptome analysis in faba bean (vicia faba l.) under ascochyta fabae infection.faba bean is an important food crop worldwide. however, progress in faba bean genomics lags far behind that of model systems due to limited availability of genetic and genomic information. using the illumina platform the faba bean transcriptome from leaves of two lines (29h and vf136) subjected to ascochyta fabae infection have been characterized. de novo transcriptome assembly provided a total of 39,185 different transcripts that were functionally annotated, and among these, 13,266 were assigne ...201526267359
genetic control of inflorescence architecture in legumes.the architecture of the inflorescence, the shoot system that bears the flowers, is a main component of the huge diversity of forms found in flowering plants. inflorescence architecture has also a strong impact on the production of fruits and seeds, and on crop management, two highly relevant agronomical traits. elucidating the genetic networks that control inflorescence development, and how they vary between different species, is essential to understanding the evolution of plant form and to bein ...201526257753
global transcriptome analysis profiles metabolic pathways in traditional herb astragalus membranaceus bge. var. mongolicus (bge.) hsiao.astragalus membranaceus bge. var. mongolicus (bge.) hsiao (a. mongolicus, family leguminosae) is one of the most important traditional chinese herbs. among many secondary metabolites it produces, the effective bioactive constituents include isoflavonoids and triterpene saponins. the genomic resources regarding the biosynthesis of these metabolites in a. mongolicus are limited. although roots are the primary material harvested for medical use, the biosynthesis of the bioactive compounds and its r ...201526099797
primary transcripts of micrornas encode regulatory peptides.micrornas (mirnas) are small regulatory rna molecules that inhibit the expression of specific target genes by binding to and cleaving their messenger rnas or otherwise inhibiting their translation into proteins. mirnas are transcribed as much larger primary transcripts (pri-mirnas), the function of which is not fully understood. here we show that plant pri-mirnas contain short open reading frame sequences that encode regulatory peptides. the pri-mir171b of medicago truncatula and the pri-mir165a ...201525807486
repression of as2 by wox family transcription factors is required for leaf development in medicago and arabidopsis.wox transcription factors are key regulators of meristematic activity in plants. the medicago wox gene, stf, functions in maintenance of leaf marginal meristem, analogous to the function of wus in the shoot apical meristem. both stf and wus directly repress as2 expression in their respective domains. ectopic expression of as2 with wus promoter leads to a narrow leaf phenotype and other phenotypes similar to the wus mutant. we also found that a wox1 prs wus triple mutant produces much narrower le ...201525807065
an ontology approach to comparative phenomics in plants.plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. because these datasets were designed for different audiences, they frequently contain language and details tailored to investigators with different research objectives and backgrounds. although phenotype comparisons across datasets have long been possible on a small scale, comprehensive queries and analyses that span a broad set of reference species, research disciplines, and knowledg ...201525774204
advances in the understanding of cuticular waxes in arabidopsis thaliana and crop species.the aerial parts of plants are covered with a cuticle, a hydrophobic layer consisting of cutin polyester and cuticular waxes that protects them from various environmental stresses. cuticular waxes mainly comprise very long chain fatty acids and their derivatives such as aldehydes, alkanes, secondary alcohols, ketones, primary alcohols, and wax esters that are also important raw materials for the production of lubricants, adhesives, cosmetics, and biofuels. the major function of cuticular waxes i ...201525693495
genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in brachypodium distachyon.in eukaryotes, alternative splicing (as) promotes transcriptome and proteome diversity. the extent of genome-wide as changes occurring during a plant-microbe interaction is largely unknown. here, using high-throughput, paired-end rna sequencing, we generated an isoform-level spliceome map of brachypodium distachyon infected with panicum mosaic virus and its satellite virus. overall, we detected ∼44,443 transcripts in b. distachyon, ∼30% more than those annotated in the reference genome. expressi ...201525634987
acquisition and loss of desiccation tolerance in seeds: from experimental model to biological relevance.besides being an important model to study desiccation tolerance, the induction of desiccation tolerance in germinated seeds may also play an ecological role in seedling establishment. desiccation tolerance (dt) is the ability of certain organisms to survive extreme water losses without accumulation of lethal damage. this was a key feature in the conquering of dry land and is currently found in all taxa including bacteria, fungi, roundworms and plants. not surprisingly, studies in various fields ...201525567203
abscisic acid: hidden architect of root system structure.plants modulate root growth in response to changes in the local environment, guided by intrinsic developmental genetic programs. the hormone abscisic acid (aba) mediates responses to different environmental factors, such as the presence of nitrate in the soil, water stress and salt, shaping the structure of the root system by regulating the production of lateral roots as well as controlling root elongation by modulating cell division and elongation. curiously, aba controls different aspects of r ...201527135341
prediction of plant pre-micrornas and their micrornas in genome-scale sequences using structure-sequence features and support vector machine.micrornas (mirnas) are a family of non-coding rnas approximately 21 nucleotides in length that play pivotal roles at the post-transcriptional level in animals, plants and viruses. these molecules silence their target genes by degrading transcription or suppressing translation. studies have shown that mirnas are involved in biological responses to a variety of biotic and abiotic stresses. identification of these molecules and their targets can aid the understanding of regulatory processes. recent ...201425547126
abscisic acid promotes pre-emergence stages of lateral root development in medicago truncatula.the plant root system is important for plant anchorage and nutrition. among the different characteristics of the root system, root branching is a major factor of plasticity and adaptation to changing environments. indeed, many biotic and abiotic stresses, such as drought or symbiotic interactions, influence root branching. many studies concerning root development and root branching were performed on the model plant arabidopsis thaliana, but this model plant has a very simplified root structure a ...201525517945
plant omics data center: an integrated web repository for interspecies gene expression networks with nlp-based curation.comprehensive integration of large-scale omics resources such as genomes, transcriptomes and metabolomes will provide deeper insights into broader aspects of molecular biology. for better understanding of plant biology, we aim to construct a next-generation sequencing (ngs)-derived gene expression network (gen) repository for a broad range of plant species. so far we have incorporated information about 745 high-quality mrna sequencing (mrna-seq) samples from eight plant species (arabidopsis thal ...201525505034
sulfate transporters in the plant's response to drought and salinity: regulation and possible functions.drought and salinity are two frequently combined abiotic stresses that affect plant growth, development, and crop productivity. sulfate, and molecules derived from this anion such as glutathione, play important roles in the intrinsic responses of plants to such abiotic stresses. therefore, understanding how plants facing environmental constraints re-equilibrate the flux of sulfate between and within different tissues might uncover perspectives for improving tolerance against abiotic stresses. in ...201425400648
comparative genomic and transcriptomic analysis of terpene synthases in arabidopsis and medicago.this study provides a timely comparative genomic and transcriptomic analysis of the terpene synthase (tps) gene family in medicago truncatula (bears glandular and non-glandular trichomes) and arabidopsis thaliana (bears non-glandular trichomes). the authors' efforts aimed to gain insight into tps function, phylogenetic relationships and the role of trichomes in terpene biosynthesis and function. in silico analysis identified 33 and 23 putative full-length tps genes in arabidopsis and medicago, r ...201425075527
genome-wide determination of poly(a) sites in medicago truncatula: evolutionary conservation of alternative poly(a) site choice.alternative polyadenylation (apa) plays an important role in the post-transcriptional regulation of gene expression. little is known about how apa sites may evolve in homologous genes in different plant species. to this end, comparative studies of apa sites in different organisms are needed. in this study, a collection of poly(a) sites in medicago truncatula, a model system for legume plants, has been generated and compared with apa sites in arabidopsis thaliana.201425048171
characterization of five subgroups of the sieve element occlusion gene family in glycine max reveals genes encoding non-forisome p-proteins, forisomes and forisome tails.p-proteins are structural phloem proteins discussed to be involved in the rapid sealing of injured sieve elements. p-proteins are found in all dicotyledonous and some monocotyledonous plants, but additional crystalloid p-proteins, known as forisomes, have evolved solely in the fabaceae. both types are encoded by members of the sieve element occlusion (seo) gene family, which comprises seven phylogenetic subgroups. the fabaceae-specific subgroup 1 contains genes encoding forisome subunits in e.g. ...201424928491
a medicago truncatula h+-pyrophosphatase gene, mtvp1, improves sucrose accumulation and anthocyanin biosynthesis in potato (solanum tuberosum l.).we recently cloned mtvp1, a type i vacuolar-type h(+)-translocating inorganic pyrophosphatase from medicago truncatula. in the present study, we investigated the cellular location and the function of this h(+)-ppase in arabidopsis and potato (solanum tuberosum l.). an mtvp1::enhanced green fluorescent protein fusion was constructed, which localized to the plasma membrane of onion epidermal cells. transgenic arabidopsis thaliana overexpressing mtvp1 had more robust root systems and redder shoots ...201424854441
study on folate binding domain of dihydrofolate reductase in different plant species and human beings.data base (ncbi and tigr) searches are made to retrieve protein sequences of different plant species namely medicago truncatula, pisum sativum, ricinus communis, arabidopsis thaliana, vitis vinifera, glycine max, daucus carota, oryza sativa japonica group, arabidopsis lyrata subsp. lyrata, brachypodium distachyon, oryza sativa indica group, zea mays and careful alignment of derived sequences shows 95% or higher identity. similarly, dhfr sequence of human being is also retrieved from ncbi. a phyl ...201424616563
est-snp discovery and dense genetic mapping in lentil (lens culinaris medik.) enable candidate gene selection for boron tolerance.large-scale snp discovery and dense genetic mapping in a lentil intraspecific cross permitted identification of a single chromosomal region controlling tolerance to boron toxicity, an important breeding objective. lentil (lens culinaris medik.) is a highly nutritious food legume crop that is cultivated world-wide. until recently, lentil has been considered a genomic 'orphan' crop, limiting the feasibility of marker-assisted selection strategies in breeding programs. the present study reports on ...201424370962
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
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
overexpression of medicago svp genes causes floral defects and delayed flowering in arabidopsis but only affects floral development in medicago.the mads-domain transcription factor short vegetative phase plays a key role as a repressor of the transition to flowering and as a regulator of early floral development in arabidopsis thaliana (arabidopsis). however, no flowering-time repressors have been functionally identified in the model legume medicago truncatula (medicago). in this study, phylogenetic analysis of two closely-related mtsvp-like sequences, mtsvp1 and mtsvp2, showed that their predicted proteins clustered together within the ...201424249713
lateral root formation and patterning in medicago truncatula.the plant root system is crucial for anchorage and nutrition, and has a major role in plant adaptation, as well as in interactions with soil micro-organisms. despite the agronomical and ecological importance of legume plants, whose roots can interact symbiotically with soil bacteria called rhizobia that fix atmospheric dinitrogen, and the evidence that lateral root (lr) development programmes are intercepted and influenced by symbiotic organisms, very little is known concerning the cellular and ...201424148318
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
early transcriptional responses to mercury: a role for ethylene in mercury-induced stress.understanding the cellular mechanisms of plant tolerance to mercury (hg) is important for developing phytoremediation strategies of hg-contaminated soils. the early responses of alfalfa (medicago sativa) seedlings to hg were studied using transcriptomics analysis. a medicago truncatula microarray was hybridized with high-quality root rna from m. sativa treated with 3 μm hg for 3, 6 and 24 h. the transcriptional pattern data were complementary to the measurements of root growth inhibition, lipid ...201424033367
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
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
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
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
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
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
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
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
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
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
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
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
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
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
the re-establishment of desiccation tolerance in germinated arabidopsis thaliana seeds and its associated transcriptome.the combination of robust physiological models with "omics" studies holds promise for the discovery of genes and pathways linked to how organisms deal with drying. here we used a transcriptomics approach in combination with an in vivo physiological model of re-establishment of desiccation tolerance (dt) in arabidopsis thaliana seeds. we show that the incubation of desiccation sensitive (ds) germinated arabidopsis seeds in a polyethylene glycol (peg) solution re-induces the mechanisms necessary f ...201122195004
mining functional microsatellites in legume unigenes.highly polymorphic and transferable microsatellites (ssrs) are important for comparative genomics, genome analysis and phylogenetic studies. development of novel species-specific microsatellite markers remains a costly and labor-intensive project. therefore, interest has been shifted from genomic to genic markers owing to their high inter-species transferability as they are developed from conserved coding regions of the genome. this study concentrates on comparative analysis of genic microsatell ...201122125396
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
comparative analysis of mirnas and their targets across four plant species.microrna (mirna) mediated regulation of gene expression has been recognized as a major posttranscriptional regulatory mechanism also in plants. we performed a comparative analysis of mirnas and their respective gene targets across four plant species: arabidopsis thaliana (ath), medicago truncatula(mtr), brassica napus (bna), and chlamydomonas reinhardtii (cre).201122067256
whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume medicago truncatula.medicago truncatula is a model for investigating legume genetics, including the genetics and evolution of legume-rhizobia symbiosis. we used whole-genome sequence data to identify and characterize sequence polymorphisms and linkage disequilibrium (ld) in a diverse collection of 26 m. truncatula accessions. our analyses reveal that m. truncatula harbors both higher diversity and less ld than soybean (glycine max) and exhibits patterns of ld and recombination similar to arabidopsis thaliana. the p ...201121949378
standardizing seed dormancy research.seeds are very attractive and convenient for molecular genetic studies that challenge principal biological phenomena related to the initiation and suppression of growth (e.g., germination and dormancy, respectively). the number of reports in this field is rapidly expanding. seed dormancy is a widely misinterpreted biological attribute. one of the main reasons is the general neglect of reliable dormancy assays; often, the sole criterion of current dormancy assays is the total germination of a see ...201121898248
the mitochondrial proteome of the model legume medicago truncatula.legumes carry out special biochemical functions, e.g. the fixation of molecular nitrogen based on a symbiosis with proteobacteria. at the cellular level, this symbiosis has to be implemented into the energy metabolism of the host cell. to provide a basis for future analyses, we have characterized the protein complement of mitochondria of the model legume medicago truncatula using two-dimensional isoelectric focussing (ief) and blue-native (bn)-sds-page. while the ief reference map resulted mainl ...201121893218
durable broad-spectrum powdery mildew resistance in pea er1 plants is conferred by natural loss-of-function mutations in psmlo1.loss-of-function alleles of plant-specific mlo (mildew resistance locus o) genes confer broad-spectrum powdery mildew resistance in monocot (barley) and dicot (arabidopsis thaliana, tomato) plants. recessively inherited powdery mildew resistance in pea (pisum sativum) er1 plants is, in many aspects, reminiscent of mlo-conditioned powdery mildew immunity, yet the underlying gene has remained elusive to date. we used a polymerase chain reaction (pcr)-based approach to amplify a candidate mlo cdna ...201121726385
developmental analysis of a medicago truncatula smooth leaf margin1 mutant reveals context-dependent effects on compound leaf development.compound leaf development requires highly regulated cell proliferation, differentiation, and expansion patterns. we identified loss-of-function alleles at the smooth leaf margin1 (slm1) locus in medicago truncatula, a model legume species with trifoliate adult leaves. slm1 encodes an auxin efflux carrier protein and is the ortholog of arabidopsis thaliana pin-formed1 (pin1). auxin distribution is impaired in the slm1 mutant, resulting in pleiotropic phenotypes in different organs. the most strik ...201121693694
the medicago flowering locus t homolog, mtfta1, is a key regulator of flowering time.flowering locus t (ft) genes encode proteins that function as the mobile floral signal, florigen. in this study, we characterized five ft-like genes from the model legume, medicago (medicago truncatula). the different ft genes showed distinct patterns of expression and responses to environmental cues. three of the ft genes (mtfta1, mtftb1, and mtftc) were able to complement the arabidopsis (arabidopsis thaliana) ft-1 mutant, suggesting that they are capable of functioning as florigen. mtfta1 is ...201121685176
developing a method for customized induction of flowering.the ability to induce flowering on demand is of significant biotechnological interest. ft protein has been recently identified as an important component of the mobile flowering hormone, florigen, whose function is conserved across the plant kingdom. we therefore focused on manipulation of both endogenous and heterologous ft genes to develop a floral induction system where flowering would be inhibited until it was induced on demand. the concept was tested in the model plant arabidopsis thaliana ( ...201121481273
evolution of the number of lrrs in plant disease resistance genes.the largest group of plant resistance (r) genes contain the regions that encode the nucleotide-binding site (nbs) and leucine-rich repeat (lrr) domains (nbs-lrr genes). to gain new resistance, amino acid substitutions and changes in number of the lrrs that recognize the presence of pathogens are considered important. in this study, we focus on the evolution of the number of lrrs and analyze the genome data of five plant species, arabidopsis thaliana, oryza sativa, medicago truncatula, lotus japo ...201121442326
plantmirnapred: efficient classification of real and pseudo plant pre-mirnas.micrornas (mirnas) are a set of short (21-24 nt) non-coding rnas that play significant roles as post-transcriptional regulators in animals and plants. while some existing methods use comparative genomic approaches to identify plant precursor mirnas (pre-mirnas), others are based on the complementarity characteristics between mirnas and their target mrnas sequences. however, they can only identify the homologous mirnas or the limited complementary mirnas. furthermore, since the plant pre-mirnas a ...201121441575
a stress-associated protein containing a20/an1 zing-finger domains expressed in medicago truncatula seeds.mtsap1 (medicago truncatula stress-associated protein 1) was revealed as a down-regulated gene by suppressive subtractive hybridization between two mrna populations of embryo axes harvested before and after radicle emergence. mtsap1 is the first gene encoding a sap with a20 and an1 zinc-finger domains characterized in m. truncatula. mtsap1 protein shares 54% and 62% homology with atsap7 (arabidopsis thaliana) and osisap8 (oryza sativa) respectively, with in particular a strong homology in the a2 ...201121296585
the pea gigas gene is a flowering locus t homolog necessary for graft-transmissible specification of flowering but not for responsiveness to photoperiod.garden pea (pisum sativum) was prominent in early studies investigating the genetic control of flowering and the role of mobile flowering signals. in view of recent evidence that genes in the flowering locus t (ft) family play an important role in generating mobile flowering signals, we isolated the ft gene family in pea and examined the regulation and function of its members. comparison with medicago truncatula and soybean (glycine max) provides evidence of three ancient subclades (fta, ftb, an ...201121282524
mutation of wrky transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants.stems of dicotyledonous plants consist of an outer epidermis, a cortex, a ring of secondarily thickened vascular bundles and interfascicular cells, and inner pith parenchyma cells with thin primary walls. it is unclear how the different cell layers attain and retain their identities. here, we show that wrky transcription factors are in part responsible for the parenchymatous nature of the pith cells in dicotyledonous plants. we isolated mutants of medicago truncatula and arabidopsis thaliana wit ...201021135241
genome-wide investigation reveals high evolutionary rates in annual model plants.rates of molecular evolution vary widely among species. while significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood. in plants, annual/perennial life history traits have long been suspected to influence the evolutionary rates at the molecular level. to date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. to evaluate the possible heterogeneity in evolu ...201021062446
molecular and phylogenetic characterization of the sieve element occlusion gene family in fabaceae and non-fabaceae plants.the phloem of dicotyledonous plants contains specialized p-proteins (phloem proteins) that accumulate during sieve element differentiation and remain parietally associated with the cisternae of the endoplasmic reticulum in mature sieve elements. wounding causes p-protein filaments to accumulate at the sieve plates and block the translocation of photosynthate. specialized, spindle-shaped p-proteins known as forisomes that undergo reversible calcium-dependent conformational changes have evolved ex ...201020932300
conservation in function of a scar/wave component during infection thread and root hair growth in medicago truncatula.nitrogen-fixing symbioses of plants are often associated with bacterially infected nodules where nitrogen fixation occurs. the plant host facilitates bacterial infection with the formation of infection threads, unique structures associated with these symbioses, which are invaginations of the host cell with the capability of traversing cellular junctions. here, we show that the infection thread shares mechanistic similarities to polar-growing cells, because the required for infection thread (rit) ...201020731530
syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (phaseolus vulgaris l.).molecular linkage maps are an important tool for gene discovery and cloning, crop improvement, further genetic studies, studies on diversity and evolutionary history, and cross-species comparisons. linkage maps differ in both the type of marker and type of population used. in this study, gene-based markers were used for mapping in a recombinant inbred (ri) population of phaseolus vulgaris l. p. vulgaris, common dry bean, is an important food source, economic product, and model organism for the l ...201020607211
walls are thin 1 (wat1), an arabidopsis homolog of medicago truncatula nodulin21, is a tonoplast-localized protein required for secondary wall formation in fibers.by combining zinnia elegans in vitro tracheary element genomics with reverse genetics in arabidopsis, we have identified a new upstream component of secondary wall formation in xylary and interfascicular fibers. walls are thin 1 (wat1), an arabidopsis thaliana homolog of medicago truncatula nodulin 21 (mtn21), encodes a plant-specific, predicted integral membrane protein, and is a member of the plant drug/metabolite exporter (p-dme) family (transporter classification number: tc 2.a.7.3). althoug ...201020497379
comparison of homoeolocus organisation in paired bac clones from white clover (trifolium repens l.) and microcolinearity with model legume species.white clover (trifolium repens l.) is an outbreeding allotetraploid species and an important forage legume in temperate grassland agriculture. comparison of sub-genome architecture and study of nucleotide sequence diversity within allopolyploids provides insight into evolutionary divergence mechanisms, and is also necessary for the development of whole-genome sequencing strategies. this study aimed to evaluate the degree of divergence between the o and p' sub-genomes of white clover through sequ ...201020492736
an integrated transcriptome atlas of the crop model glycine max, and its use in comparative analyses in plants.soybean (glycine max l.) is a major crop providing an important source of protein and oil, which can also be converted into biodiesel. a major milestone in soybean research was the recent sequencing of its genome. the sequence predicts 69,145 putative soybean genes, with 46,430 predicted with high confidence. in order to examine the expression of these genes, we utilized the illumina solexa platform to sequence cdna derived from 14 conditions (tissues). the result is a searchable soybean gene ex ...201020408999
an nac transcription factor orchestrates multiple features of cell wall development in medicago truncatula.to identify genes controlling secondary cell wall biosynthesis in the model legume medicago truncatula, we screened a tnt1 retrotransposon insertion mutant population for plants with altered patterns of lignin autofluorescence. from more than 9000 r1 plants screened, four independent lines were identified with a total lack of lignin in the interfascicular region. the mutants also showed loss of lignin in phloem fibers, reduced lignin in vascular elements, failure in anther dehiscence and absence ...201020408998
flavonoids: new roles for old molecules.flavonoids are ubiquitous in the plant kingdom and have many diverse functions including defense, uv protection, auxin transport inhibition, allelopathy, and flower coloring. interestingly, these compounds also have considerable biological activity in plant, animal and bacterial systems - such broad activity is accomplished by few compounds. yet, for all the research over the last three decades, many of the cellular targets of these secondary metabolites are unknown. the many mutants available i ...201020074144
dominance induction of fruitlet shedding in malus x domestica (l. borkh): molecular changes associated with polar auxin transport.apple fruitlet abscission is induced by dominance, a process in which hormones such as auxin, cytokinins and strigolactone play a pivotal role. the response to these hormones is controlled by transcription regulators such as aux/iaa and arr, whereas auxin transport is controlled by influx and efflux carriers.200919941659
construction of a rice glycosyltransferase phylogenomic database and identification of rice-diverged glycosyltransferases.glycosyltransferases (gts; ec 2.4.x.y) constitute a large group of enzymes that form glycosidic bonds through transfer of sugars from activated donor molecules to acceptor molecules. gts are critical to the biosynthesis of plant cell walls, among other diverse functions. based on the carbohydrate-active enzymes (cazy) database and sequence similarity searches, we have identified 609 potential gt genes (loci) corresponding to 769 transcripts (gene models) in rice (oryza sativa), the reference mon ...200819825588
full-size abc transporters from the abcg subfamily in medicago truncatula.full-size atp-binding cassette (abc) transporters belonging to the abcg subfamily are unique for plants and fungi. there is growing evidence that certain of these proteins play a role in plant defense or signaling systems. as yet, a complete set of full-size abcg protein genes has been inventoried and classified in only two plants: arabidopsis thaliana and oryza sativa. recently, a domain-based clustering analysis has predicted the presence of at least 12 genes encoding such proteins in the lotu ...200919589068
microcollinearity in an ethylene receptor coding gene region of the coffea canephora genome is extensively conserved with vitis vinifera and other distant dicotyledonous sequenced genomes.coffea canephora, also called robusta, belongs to the rubiaceae, the fourth largest angiosperm family. this diploid species (2x = 2n = 22) has a fairly small genome size of approximately 690 mb and despite its extreme economic importance, particularly for developing countries, knowledge on the genome composition, structure and evolution remain very limited. here, we report the 160 kb of the first c. canephora bacterial artificial chromosome (bac) clone ever sequenced and its fine analysis.200919243618
transcriptional regulation and signaling in phosphorus starvation: what about legumes?the availability of soil phosphorus (p), an essential element, is one of the most important requirements for plant growth and crop production. the morphological and physiological adaptations evolved by plants to cope with p starvation have been well characterized. several p deficiency plant responses are regulated at the transcriptional level. microarray analysis has generated valuable information on global gene expression in arabidopsis thaliana grown under p-stress. despite the identification ...200819017108
gfp tagging of sieve element occlusion (seo) proteins results in green fluorescent forisomes.forisomes are ca(2+)-driven, atp-independent contractile protein bodies that reversibly occlude sieve elements in faboid legumes. they apparently consist of at least three proteins; potential candidates have been described previously as 'for' proteins. we isolated three genes from medicago truncatula that correspond to the putative forisome proteins and expressed their green fluorescent protein (gfp) fusion products in vicia faba and glycine max using the composite plant methodology. in both spe ...200818784195
functional analysis of ljsut4, a vacuolar sucrose transporter from lotus japonicus.sucrose transporters in the sut family are important for phloem loading and sucrose uptake into sink tissues. the recent localization of type iii suts atsut4 and hvsut2 to the vacuole membrane suggests that suts also function in vacuolar sucrose transport. the transport mechanism of type iii suts has not been analyzed in detail. ljsut4, a type iii sucrose transporter homolog from lotus japonicus, is expressed in nodules and its transport activity has not been previously investigated. in this rep ...200818618272
substitution of the gene for chloroplast rps16 was assisted by generation of a dual targeting signal.organelle (mitochondria and chloroplasts in plants) genomes lost a large number of genes after endosymbiosis occurred. even after this major gene loss, organelle genomes still lose their own genes, even those that are essential, via gene transfer to the nucleus and gene substitution of either different organelle origin or de novo genes. gene transfer and substitution events are important processes in the evolution of the eukaryotic cell. gene loss is an ongoing process in the mitochondria and ch ...200818453549
characterization and comparison of intron structure and alternative splicing between medicago truncatula, populus trichocarpa, arabidopsis and rice.alignment of transcripts and genome sequences yielded a set of alternatively spliced transcripts in four angiosperm genomes: three dicotyledon species medicago truncatula (medicago), populus trichocarpa (poplar) and arabidopsis thaliana (arabidopsis), and the monocotyledon oryzae sativa (rice). intron retention was the predominant mode of alternative splicing (as) in each species, consistent with previous reports for arabidopsis and rice. we analyzed the structure of 5'-splice junctions and obse ...200818438730
low-coverage massively parallel pyrosequencing of cdnas enables proteomics in non-model species: comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes.proteomics is a valuable tool for establishing and comparing the protein content of defined tissues, cell types, or subcellular structures. its use in non-model species is currently limited because the identification of peptides critically depends on sequence databases. in this study, we explored the potential of a preliminary cdna database for the non-model species pisum sativum created by a small number of massively parallel pyrosequencing (mpss) runs for its use in proteomics and compared it ...200818394738
sub-lethal levels of electric current elicit the biosynthesis of plant secondary metabolites.many secondary metabolites that are normally undetectable or in low amounts in healthy plant tissue are synthesized in high amounts in response to microbial infection. various abiotic and biotic agents have been shown to mimic microorganisms and act as elicitors of the synthesis of these plant compounds. in the present study, sub-lethal levels of electric current are shown to elicit the biosynthesis of secondary metabolites in transgenic and non-transgenic plant tissue. the production of the phy ...201518331050
fractionation of synteny in a genomic region containing tandemly duplicated genes across glycine max, medicago truncatula, and arabidopsis thaliana.extended comparison of gene sequences found on homeologous soybean bacterial artificial chromosomes to medicago truncatula and arabidopsis thaliana genomic sequences demonstrated a network of synteny within conserved regions interrupted by gene addition and/or deletions. consolidation of gene order among all 3 species provides a picture of ancestral gene order. the observation supports a genome history of fractionation resulting from gene loss/addition and rearrangement. in all 3 species, cluste ...200818316321
heterologous expression of iap1, a seed protein from bean modified by indole-3-acetic acid, in arabidopsis thaliana and medicago truncatula.the seed protein iap1 from bean (pviap1; phaseolus vulgaris l.) that is modified by the phytohormone indole-3-acetic acid (iaa) was heterologously expressed in the two reference plant species arabidopsis thaliana and medicago truncatula. for the transformation of medicago we devised a novel protocol using seedling infiltration. when pviap1 was overexpressed under the control of the constitutive 35scamv promoter in arabidopsis, the plants showed signs of earlier bolting and enhanced branching. ex ...200818097685
root exudates regulate soil fungal community composition and diversity.plants are in constant contact with a community of soil biota that contains fungi ranging from pathogenic to symbiotic. a few studies have demonstrated a critical role of chemical communication in establishing highly specialized relationships, but the general role for root exudates in structuring the soil fungal community is poorly described. this study demonstrates that two model plant species (arabidopsis thaliana and medicago truncatula) are able to maintain resident soil fungal populations b ...200818083870
planttribes: a gene and gene family resource for comparative genomics in plants.the planttribes database (http://fgp.huck.psu.edu/tribe.html) is a plant gene family database based on the inferred proteomes of five sequenced plant species: arabidopsis thaliana, carica papaya, medicago truncatula, oryza sativa and populus trichocarpa. we used the graph-based clustering algorithm mcl [van dongen (technical report ins-r0010 2000) and enright et al. (nucleic acids res. 2002; 30: 1575-1584)] to classify all of these species' protein-coding genes into putative gene families, calle ...200818073194
riboregulators in plant development.npcrna (non-protein-coding rnas) are an emerging class of regulators, so-called riboregulators, and include a large diversity of small rnas [mirnas (micrornas)/sirnas (small interfering rnas)] that are involved in various developmental processes in plants and animals. in addition, several other npcrnas encompassing various transcript sizes (up to several kilobases) have been identified using different genomic approaches. much less is known about the mechanism of action of these other classes of ...200718031282
identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant medicago truncatula.the nucleotide-binding site (nbs)-leucine-rich repeat (lrr) gene family accounts for the largest number of known disease resistance genes, and is one of the largest gene families in plant genomes. we have identified 333 nonredundant nbs-lrrs in the current medicago truncatula draft genome (mt1.0), likely representing 400 to 500 nbs-lrrs in the full genome, or roughly 3 times the number present in arabidopsis (arabidopsis thaliana). although many characteristics of the gene family are similar to ...200817981990
tandem duplications of a degenerated gtp-binding domain at the origin of gtpase receptors toc159 and thylakoidal srp.the evolutionary origin of some nuclear encoded proteins that translocate proteins across the chloroplast envelope remains unknown. therefore, sequences of gtpase proteins constituting the arabidopsis thaliana translocon at the outer membrane of chloroplast (attoc) complexes were analyzed by means of hca. in particular, attoc159 and related proteins (attoc132, attoc120, and attoc90) do not have proven homologues of prokaryotic or eukaryotic ancestry. we established that the three domains commonl ...200717950698
computer-vision analysis of seedling responses to light and gravity.measuring the effects of mutation, natural variation or treatment on the development of plant form is often complicated by the shapes, dynamics or small size of the organismal structures under study. this limits accuracy and throughput of measurement and thereby limits progress toward understanding the underlying gene networks and signaling systems. a computer-vision platform based on electronic image capture and shape-analysis algorithms was developed as an alternative to the mostly manual meth ...200717711415
cgkb: an annotation knowledge base for cowpea (vigna unguiculata l.) methylation filtered genomic genespace sequences.cowpea [vigna unguiculata (l.) walp.] is one of the most important food and forage legumes in the semi-arid tropics because of its ability to tolerate drought and grow on poor soils. it is cultivated mostly by poor farmers in developing countries, with 80% of production taking place in the dry savannah of tropical west and central africa. cowpea is largely an underexploited crop with relatively little genomic information available for use in applied plant breeding. the goal of the cowpea genomic ...200717445272
genebins: a database for classifying gene expression data, with application to plant genome arrays.to interpret microarray experiments, several ontological analysis tools have been developed. however, current tools are limited to specific organisms.200717349060
validation of in silico-predicted genic snps in white clover (trifolium repens l.), an outbreeding allopolyploid species.white clover (trifolium repens l.) is an obligate outbreeding allotetraploid forage legume. gene-associated snps provide the optimum genetic system for improvement of such crop species. an est resource obtained from multiple cdna libraries constructed from numerous genotypes of a single cultivar has been used for in silico snp discovery and validation. a total of 58 from 236 selected sequence clusters (24.5%) were fully validated as containing polymorphic snps by genotypic analysis across the pa ...200717216492
cyp74c3 and cyp74a1, plant cytochrome p450 enzymes whose activity is regulated by detergent micelle association, and proposed new rules for the classification of cyp74 enzymes.cyp74c3 (cytochrome p450 subfamily 74c3), an hpl (hydroperoxide lyase) from medicago truncatula (barrel medic), and cyp74a1, an aos (allene oxide synthase) from arabidopsis thaliana, are key membrane-associated p450 enzymes in plant oxylipin metabolism. both recombinant detergent-free enzymes are monomeric proteins with dual specificity and very low enzyme activity that can be massively activated with detergent. this effect is a result of the formation of a complex between the protein monomer an ...200617073790
extending mapman: application to legume genome arrays.based on a gene classification into hierarchical categories ('bins'), mapman was originally developed to display arabidopsis thaliana gene expression in a functional context. we have created a bioinformatics system to extend mapman to any organism by using a new bin structure based on the kegg database. gene sequences are assigned to this ontology by homology relationships in four reference databases: kegg, cog, swiss-prot and gene ontology. we applied this system to tailor mapman to the genechi ...200617046975
phosphoproteins analysis in plants: a proteomic approach.the study of phosphoproteome on a global scale represents one of the challenges in the post-genomic era. here, we propose an integrated procedure starting from the crude protein extract, that consists of sequential purification steps, and ending up in the identification of phosphorylation sites. this involves (i) an enrichment in phosphoproteins with a commercially available chromatography matrix, (ii) a 2-d gel analysis of the enriched fraction followed by the selective staining with the phosph ...200616962150
medicago truncatula syntaxin syp132 defines the symbiosome membrane and infection droplet membrane in root nodules.symbiotic association of legume plants with rhizobia bacteria culminates in organogenesis of nitrogen-fixing root nodules. in indeterminate nodules, plant cells accommodate rhizobial infection by enclosing each bacterium in a membrane-bound, organelle-like compartment called the symbiosome. numerous symbiosomes occupy each nodule cell; therefore an enormous amount of membrane material must be delivered to the symbiosome membrane for its development and maintenance. protein delivery to the symbio ...200716944200
isolation and characterization of root-specific phosphate transporter promoters from medicago trunatula.promoters of phosphate transporter genes mtpt1 and mtpt2 of medicago truncatula were isolated by utilizing the gene-space sequence information and by screening of a genomic library, respectively. two reporter genes, beta-glucuronidase (gus) and green fluorescent protein (gfp) were placed under the control of the mtpt1 and mtpt2 promoters. these chimeric transgenes were introduced into arabidopsis thaliana and transgenic roots of m. truncatula, and expression patterns of the reporter genes were a ...200616917979
indole-3-acetic acid protein conjugates: novel players in auxin homeostasis.indole-3-acetic acid (iaa) is found in plants in both free and conjugated forms. within the group of conjugated iaa there is a unique class of proteins and peptides where iaa is attached directly to the polypeptide structure as a prosthetic group. the first gene, iap1, encoding for a protein with iaa as a prosthetic group, was cloned from bean (phaseolus vulgaris). it was shown that the expression of iap1 as a major iaa modified protein in bean seed (pviap1) was correlated to a developmental per ...200616807826
comprehensive structural analysis of the genome of red clover (trifolium pratense l.).with the aim of establishing the basic knowledge and resources needed for applied genetics, we investigated the genome structure of red clover trifolium pratense l. by a combination of cytological, genomic and genetic approaches. the deduced genome size was approximately 440 mb, as estimated by measuring the nuclear dna content by flow cytometry. seven chromosomes could be distinguished by microscopic observation of dapi stained prometaphase chromosomes and fluorescence in situ hybridization usi ...200516769692
significant microsynteny with new evolutionary highlights is detected between arabidopsis and legume model plants despite the lack of macrosynteny.the increased amount of data produced by large genome sequencing projects allows scientists to carry out important syntenic studies to a great extent. detailed genetic maps and entirely or partially sequenced genomes are compared, and macro- and microsyntenic relations can be determined for different species. in our study, the syntenic relationships between key legume plants and two model plants, arabidopsis thaliana and populus trichocarpa were investigated. the comparison of the map position o ...200516273388
the dark side of green fluorescent protein.here, severe interference of chlorophyll with green fluorescent protein (gfp) fluorescence is described for medicago (medicago truncatula), rice (oryza sativa) and arabidopsis (arabidopsis thaliana). this interference disrupts the proportional relationship between gfp content and fluorescence that is intrinsic to its use as a quantitative reporter. the involvement of chlorophyll in the loss of gfp fluorescence with leaf age was shown in vivo, by the removal of chlorophyll through etiolation or b ...200516219071
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