scholarly journals LeGOO: An Expertized Knowledge Database for the Model Legume Medicago truncatula

2019 ◽  
Vol 61 (1) ◽  
pp. 203-211 ◽  
Author(s):  
S�bastien Carr�re ◽  
Marion Verdenaud ◽  
Clare Gough ◽  
J�r�me Gouzy ◽  
Pascal Gamas
Keyword(s):  
Medicago Truncatula ◽  
Reverse Genetics ◽  
Arbuscular Mycorrhizal ◽  
Biological Information ◽  
Model Species ◽  
Model Legume ◽  
Wide Range ◽  
Legume Symbiosis ◽  
Symbiotic Nodule ◽  
Set Up

Abstract Medicago truncatula was proposed, about three decades ago, as a model legume to study the Rhizobium-legume symbiosis. It has now been adopted to study a wide range of biological questions, including various developmental processes (in particular root, symbiotic nodule and seed development), symbiotic (nitrogen-fixing and arbuscular mycorrhizal endosymbioses) and pathogenic interactions, as well as responses to abiotic stress. With a number of tools and resources set up in M. truncatula for omics, genetics and reverse genetics approaches, massive amounts of data have been produced, as well as four genome sequence releases. Many of these data were generated with heterogeneous tools, notably for transcriptomics studies, and are consequently difficult to integrate. This issue is addressed by the LeGOO (for Legume Graph-Oriented Organizer) knowledge base (https://www.legoo.org), which finds the correspondence between the multiple identifiers of the same gene. Furthermore, an important goal of LeGOO is to collect and represent biological information from peer-reviewed publications, whatever the technical approaches used to obtain this information. The information is modeled in a graph-oriented database, which enables flexible representation, with currently over 200,000 relations retrieved from 298 publications. LeGOO also provides the user with mining tools, including links to the Mt5.0 genome browser and associated information (on gene functional annotation, expression, methylome, natural diversity and available insertion mutants), as well as tools to navigate through different model species. LeGOO is, therefore, an innovative database that will be useful to the Medicago and legume community to better exploit the wealth of data produced on this model species.

Cloning, molecular characterization, and expression analysis of several red clover cDNAs

2006 ◽  
Vol 86 (2) ◽  
pp. 465-468
Author(s):  
Michael L. Sullivan ◽  
Sharon L. Thoma
Keyword(s):  
Medicago Truncatula ◽  
Expression Analysis ◽  
Binding Protein ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Molecular Genetic ◽  
Red Clover ◽  
Model Legume ◽  
Gene Set ◽  
Wide Range

To begin gathering information regarding nucleotide sequence similarity between red clover genes and other plant species, especially the model legume Medicago truncatula, several random red clover cDNAs were sequenced. The analyzed cDNAs included genes encoding actin; several proteins involved in photosynthesis including PsaH, PsbR, PsbX, early light-induced protein (ELIP), ferredoxin, chlorophyll a/b binding protein; fructose-bisphosphate aldolase;chloroplastic superoxide dismutase; and GTP-binding protein typA. The gene set had a median sequence identity of 92% with their counterparts from M. truncatula, suggesting its available genomics tools can be applied to red clover. An expression analysis of the gene set in various red clover tissues indicates the genes show a wide range of expression patterns. Consequently, this set of cDNAs and associated data are proving useful as controls in molecular genetic experiments involving red clover. Key words: Red clover, Trifolium pratense, Medicago truncatula, forage legume, genomics, inquiry-based learning

Collection of mutants for functional genomics in the legume Medicago truncatula

2011 ◽  
Vol 9 (2) ◽  
pp. 174-176 ◽  
Author(s):  
O. Calderini ◽  
M. Carelli ◽  
F. Panara ◽  
E. Biazzi ◽  
C. Scotti ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Medicago Truncatula ◽  
Reverse Genetics ◽  
Plant Traits ◽  
Secondary Compounds ◽  
Flower Morphology ◽  
Ethyl Methanesulfonate ◽  
Biosynthetic Pathways ◽  
Model Species ◽  
Ems Mutagenesis

We have established mutant collections of the model species Medicago truncatula according to current protocols. In particular, we used a transposon (Tnt1) tagging method and an ethyl methanesulfonate (EMS) mutagenesis approach (TILLING). The collections were subjected to both forward and reverse genetics screenings, and several mutants were isolated that affect plant traits (e.g. shoot, root developments, flower morphology, etc.) and also biosynthetic pathways of secondary compounds (saponins and tannins). Genes responsible for some of the mutations were cloned and further characterized.

scholarly journals MtExpress, a Comprehensive and Curated RNAseq-based Gene Expression Atlas for the Model Legume Medicago truncatula

2021 ◽  
Author(s):  
Sebastien Carrere ◽  
Jerome Verdier ◽  
Pascal Gamas
Keyword(s):  
Gene Expression ◽  
Medicago Truncatula ◽  
Orthologous Gene ◽  
Model Legume ◽  
Fully Integrated ◽  
Gene Expression Atlas ◽  
Rnaseq Data ◽  
Wide Range ◽  
Complementary Resource ◽  
Expression Atlas

Abstract Although RNA sequencing has been becoming the main transcriptomic approach in the model legume Medicago truncatula, there is currently no genome-wide gene expression atlas covering the whole set of RNAseq data published for this species. Nowadays, such tool is highly valuable to provide a global view of gene expression in a wide range of conditions and tissues/organs. Here, we present MtExpress, a gene expression atlas that compiles an exhaustive set of published M. truncatula RNAseq data (https://medicago.toulouse.inrae.fr/MtExpress). MtExpress makes use of recent releases of M. truncatula genome sequence and annotation, as well as up-to-date tools to perform mapping, quality control, statistical analysis and normalization of RNAseq data. MtExpress combines semi-automated pipelines with manual re-labelling and organization of samples, to produce an attractive and user-friendly interface, fully integrated with other available Medicago genomic resources. Importantly, MtExpress is highly flexible, in terms of both queries, e.g. allowing searches with gene names and orthologous gene IDs from Arabidopsis and other legume species, and outputs, to customize visualization and redirect gene study to relevant Medicago webservers. Thanks to its semi-automated pipeline, MtExpress will be frequently updated to follow the rapid pace of M. truncatula RNAseq data publications, as well as the constant improvement of genome annotation. MtExpress also hosts legacy GeneChip expression data originally stored in the Medicago Gene Expression Atlas (MtGEA), as a very valuable and complementary resource.

scholarly journals Aeschynomene evenia, a Model Plant for Studying the Molecular Genetics of the Nod-Independent Rhizobium-Legume Symbiosis

2012 ◽  
Vol 25 (7) ◽  
pp. 851-861 ◽  
Author(s):  
Jean-François Arrighi ◽  
Fabienne Cartieaux ◽  
Spencer C. Brown ◽  
Marguerite Rodier-Goud ◽  
Marc Boursot ◽  
...  
Keyword(s):  
Lotus Japonicus ◽  
Infection Process ◽  
Ancestral State ◽  
Model Legume ◽  
Hybridization Procedure ◽  
Bradyrhizobium Sp ◽  
Thread Formation ◽  
Legume Symbiosis ◽  
Independent Process ◽  
Set Up

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 the ancestral state of the rhizobium–legume symbiosis. To decipher the mechanisms of this Nod-independent process, we propose Aeschynomene evenia as a model legume because it presents all the characteristics required for genetic and molecular analysis. It is a short-perennial and autogamous species, with a diploid and relatively small genome (2n = 20; 460 Mb/1C). A. evenia ‘IRFL6945’ is nodulated by the well-characterized photosynthetic Bradyrhizobium sp. strain ORS278 and is efficiently transformed by Agrobacterium rhizogenes. Aeschynomene evenia is genetically homozygous but polymorphic accessions were found. A manual hybridization procedure has been set up, allowing directed crosses. Therefore, it should be relatively straightforward to unravel the molecular determinants of the Nod-independent process in A. evenia. This should shed new light on the evolution of rhizobium–legume symbiosis and could have important agronomic implications.

scholarly journals MtExpress, a Comprehensive and Curated RNAseq-based Gene Expression Atlas for the Model Legume Medicago truncatula

2021 ◽  
Author(s):  
Sebastien Carrere ◽  
Jerome Verdier ◽  
Pascal Gamas
Keyword(s):  
Gene Expression ◽  
Medicago Truncatula ◽  
Orthologous Gene ◽  
Model Legume ◽  
Fully Integrated ◽  
Gene Expression Atlas ◽  
Rnaseq Data ◽  
Wide Range ◽  
Expression Atlas ◽  
Gene Study

Although RNA sequencing has been becoming the main transcriptomic approach in the model legume Medicago truncatula, there is currently no genome-wide gene expression atlas covering the whole set of RNAseq data published for this species. Nowadays, such tool is highly valuable to provide a global view of gene expression in a wide range of conditions and tissues/organs. Here, we present MtExpress, a gene expression atlas that compiles an exhaustive set of published M. truncatula RNAseq data (https://medicago.toulouse.inrae.fr/MtExpress). MtExpress makes use of recent releases of M. truncatula genome sequence and annotation, as well as up-to-date tools to perform mapping, quality control, statistical analysis and normalization of RNAseq data. MtExpress combines semi-automated pipelines with manual re-labelling and organization of samples, to produce an attractive and user-friendly interface, fully integrated with other available Medicago genomic resources. Importantly, MtExpress is highly flexible, in terms of both queries, e.g. allowing searches with gene names and orthologous gene IDs from Arabidopsis and other legume species, and outputs, to customize visualization and redirect gene study to relevant Medicago webservers. Thanks to its semi-automated pipeline, MtExpress will be frequently updated to follow the rapid pace of M. truncatula RNAseq data publications, as well as the constant improvement of genome annotation.

scholarly journals The Medicago truncatula Sucrose Synthase Gene MtSucS1 Is Activated Both in the Infected Region of Root Nodules and in the Cortex of Roots Colonized by Arbuscular Mycorrhizal Fungi

2003 ◽  
Vol 16 (10) ◽  
pp. 903-915 ◽  
Author(s):  
Natalija Hohnjec ◽  
Andreas M. Perlick ◽  
Alfred Pühler ◽  
Helge Küster
Keyword(s):  
Medicago Truncatula ◽  
Mycorrhizal Fungi ◽  
Sucrose Synthase ◽  
Root Nodules ◽  
Arbuscular Mycorrhizal ◽  
Grain Legume ◽  
Sink Strength ◽  
Cortical Cells ◽  
Model Legume ◽  
Microbial Symbionts

The MtSucS1 gene encodes a sucrose synthase (EC 2.4.1.13) in the model legume Medicago truncatula. To determine the expression pattern of this gene in different organs and in particular during root endosymbioses, we transformed M. truncatula with specific regions of MtSucS1 fused to the gusAint reporter gene. These fusions directed an induction to the vasculature of leaves, stems, and roots as well as to flowers, developing seeds, young pods, and germinating seedlings. In root nodules, strong promoter activity occurred in the infected cells of the nitrogen-fixing zone but was additionally observed in the meristematic region, the prefixing zone, and the inner cortex, including the vasculature. Concerning endomycorrhizal roots, the MtSucS1 promoter mediated strongest expression in cortical cells harboring arbuscules. Specifically in highly colonized root sections, GUS-staining was furthermore detected in the surrounding cortical cells, irrespective of a direct contact with fungal structures. In accordance with the presence of an orthologous PsSus1 gene, we observed a comparable regulation of MtSucS1 expression in the grain legume Pisum sativum in response to microbial symbionts. Unlike other members of the MtSucS gene family, the presence of rhizobial or Glomus microsymbionts significantly altered and enhanced MtSucS1 gene expression, leading us to propose that MtSucS1 is involved in generating sink-strength, not only in root nodules but also in mycorrhizal roots.

scholarly journals UGT84F9 is the major flavonoid UDP-glucuronosyltransferase in Medicago truncatula

2021 ◽  
Author(s):  
Olubu A Adiji ◽  
Maite L Docampo-Palacios ◽  
Anislay Alvarez-Hernandez ◽  
Giulio M Pasinetti ◽  
Xiaoqiang Wang ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Phase Ii ◽  
Loss Of Function ◽  
In Planta ◽  
Model Legume ◽  
Flavonoid Compounds ◽  
Wide Range ◽  
Udp Glucuronosyltransferase ◽  
Phase Ii Metabolites

Abstract Mammalian phase II metabolism of dietary plant flavonoid compounds generally involves substitution with glucuronic acid. In contrast, flavonoids mainly exist as glucose conjugates in plants, and few plant UDP-glucuronosyltransferase enzymes have been identified to date. In the model legume Medicago truncatula, the major flavonoid compounds in the aerial parts of the plant are glucuronides of the flavones apigenin and luteolin. Here we show that the M. truncatula glycosyltransferase UGT84F9 is a bi-functional glucosyl/glucuronosyl transferase in vitro, with activity against a wide range of flavonoid acceptor molecules including flavones. However, analysis of metabolite profiles in leaves and roots of M. truncatula ugt84f9 loss of function mutants revealed that the enzyme is essential for formation of flavonoid glucuronides, but not most flavonoid glucosides, in planta. We discuss the use of plant UGATs for the semi-synthesis of flavonoid phase II metabolites for clinical studies.

Settlers or Movers? The Temporality of Past Migrations, Political Inaction and its Consequences, 1945–1985

2018 ◽  
Author(s):  
Jozefien De Bock
Keyword(s):  
Temporary Workers ◽  
Guest Workers ◽  
Temporary Migration ◽  
Wide Range ◽  
Settler Societies ◽  
Future Policy ◽  
Set Up ◽  
Legal Frameworks ◽  
Temporary Migrants ◽  
Multicultural Policies

Historically, those societies that have the longest tradition in multicultural policies are settler societies. The question of how to deal with temporary migrants has only recently aroused their interest. In Europe, temporary migration programmes have a much longer history. In the period after WWII, a wide range of legal frameworks were set up to import temporary workers, who came to be known as guest workers. In the end, many of these ‘guests’ settled in Europe permanently. Their presence lay at the basis of European multicultural policies. However, when these policies were drafted, the former mobility of guest workers had been forgotten. This chapter will focus on this mobility of initially temporary workers, comparing the period of economic growth 1945-1974 with the years after the 1974 economic crisis. Further, it will look at the kind of policies that were developed towards guest workers in the era before multiculturalism. This way, it shows how their consideration as temporary residents had far-reaching consequences for the immigrants, their descendants and the receiving societies involved. The chapter will finish by suggesting a number of lessons from the past. If the mobility-gap between guest workers and present-day migrants is not as big as generally assumed, then the consequences of previous neglect should serve as a warning for future policy making.

ORAL HISTORY SOURCES AS LEARNING MATERIALS: A CASE STUDY OF THE NATIONAL UNIVERSITY OF SCIENCE AND TECHNOLOGY

2016 ◽  
Vol 3 (2) ◽  
pp. 82-93
Author(s):  
Gugulethu Shamaine Nkala ◽  
Rodreck David
Keyword(s):  
Oral History ◽  
Learning Experience ◽  
Science And Technology ◽  
Group Discussion ◽  
Human Interaction ◽  
Learning Material ◽  
Wide Range ◽  
National Archives ◽  
National University ◽  
Set Up

Knowledge presented by Oral History (OH) is unique in that it shares the tacit perspective, thoughts, opinions and understanding of the interviewee in its primary form. While teachers, lecturers and other education specialists have at their disposal a wide range of primary, secondary and tertiary sources upon which to relate and share or impart knowledge, OH presents a rich source of information that can improve the learning and knowledge impartation experience. The uniqueness of OH is presented in the following advantages of its use: it allows one to learn about the perspectives of individuals who might not otherwise appear in the historical record; it allows one to compensate for the digital age; one can learn different kinds of information; it provides historical actors with an opportunity to tell their own stories in their own words; and it offers a rich opportunity for human interaction. This article discusses the placement of oral history in the classroom set-up by investigating its use as a source of learning material presented by the National Archives of Zimbabwe to students in the Department of Records and Archives Management at the National University of Science and Technology (NUST). Interviews and a group discussion were used to gather data from an archivist at the National Archives of Zimbabwe, lecturers and students in the Department of Records and Archives Management at NUST, respectively. These groups were approached on the usability, uniqueness and other characteristics that support this type of knowledge about OH in a tertiary learning experience. The findings indicate several qualities that reflect the richness of OH as a teaching source material in a classroom set-up. It further points to weak areas that may be addressed where the source is considered a viable strategy for knowledge sharing and learning. The researchers present a possible model that can be used to champion the use of this rich knowledge source in classroom education at this university and in similar set-ups. 

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