scholarly journals Recent Advances in Medicago truncatula Genomics

2008 ◽  
Vol 2008 ◽  
pp. 1-11 ◽  
Author(s):  
Jean-Michel Ané ◽  
Hongyan Zhu ◽  
Julia Frugoli
Keyword(s):  
Medicago Truncatula ◽  
Human Population ◽  
Lotus Japonicus ◽  
Model Systems ◽  
Biological Information ◽  
Comparative Genomic ◽  
Legume Nodulation ◽  
Symbiotic Interactions ◽  
Genomic Tools ◽  
Consistent Increase

Legume rotation has allowed a consistent increase in crop yield and consequently in human population since the antiquity. Legumes will also be instrumental in our ability to maintain the sustainability of our agriculture while facing the challenges of increasing food and biofuel demand. Medicago truncatula and Lotus japonicus have emerged during the last decade as two major model systems for legume biology. Initially developed to dissect plant-microbe symbiotic interactions and especially legume nodulation, these two models are now widely used in a variety of biological fields from plant physiology and development to population genetics and structural genomics. This review highlights the genetic and genomic tools available to the M. truncatula community. Comparative genomic approaches to transfer biological information between model systems and legume crops are also discussed.

LegumeDB1 bioinformatics resource: comparative genomic analysis and novel cross-genera marker identification in lupin and pasture legume species

Genome ◽  
2006 ◽  
Vol 49 (6) ◽  
pp. 689-699 ◽  
Author(s):  
P Moolhuijzen ◽  
M Cakir ◽  
A Hunter ◽  
D Schibeci ◽  
A Macgregor ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expressed Sequence Tags ◽  
Lotus Japonicus ◽  
Comparative Genomic ◽  
Legume Species ◽  
Model Legume ◽  
Bioinformatics Resource ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Pasture Legume

The identification of markers in legume pasture crops, which can be associated with traits such as protein and lipid production, disease resistance, and reduced pod shattering, is generally accepted as an important strategy for improving the agronomic performance of these crops. It has been demonstrated that many quantitative trait loci (QTLs) identified in one species can be found in other plant species. Detailed legume comparative genomic analyses can characterize the genome organization between model legume species (e.g., Medicago truncatula, Lotus japonicus) and economically important crops such as soybean (Glycine max), pea (Pisum sativum), chickpea (Cicer arietinum), and lupin (Lupinus angustifolius), thereby identifying candidate gene markers that can be used to track QTLs in lupin and pasture legume breeding. LegumeDB is a Web-based bioinformatics resource for legume researchers. LegumeDB analysis of Medicago truncatula expressed sequence tags (ESTs) has identified novel simple sequence repeat (SSR) markers (16 tested), some of which have been putatively linked to symbiosome membrane proteins in root nodules and cell-wall proteins important in plant-pathogen defence mechanisms. These novel markers by preliminary PCR assays have been detected in Medicago truncatula and detected in at least one other legume species, Lotus japonicus, Glycine max, Cicer arietinum, and (or) Lupinus angustifolius (15/16 tested). Ongoing research has validated some of these markers to map them in a range of legume species that can then be used to compile composite genetic and physical maps. In this paper, we outline the features and capabilities of LegumeDB as an interactive application that provides legume genetic and physical comparative maps, and the efficient feature identification and annotation of the vast tracks of model legume sequences for convenient data integration and visualization. LegumeDB has been used to identify potential novel cross-genera polymorphic legume markers that map to agronomic traits, supporting the accelerated identification of molecular genetic factors underpinning important agronomic attributes in lupin.Key words: legumes, comparative genomics, bioinformatics, expressed sequence tags (ESTs), simple sequence repeats (SSRs).

Versatile and Dynamic Symbioses Between Insects and Burkholderia Bacteria

2020 ◽  
Vol 65 (1) ◽  
pp. 145-170 ◽  
Author(s):  
Martin Kaltenpoth ◽  
Laura V. Flórez
Keyword(s):  
Mixed Mode ◽  
Evolutionary Dynamics ◽  
Large Fraction ◽  
Pathogenic Fungi ◽  
Model Systems ◽  
Diverse Group ◽  
Symbiotic Associations ◽  
Symbiotic Interactions ◽  
Nutritional Benefits ◽  
Symbiont Acquisition

Symbiotic associations with microorganisms represent major sources of ecological and evolutionary innovations in insects. Multiple insect taxa engage in symbioses with bacteria of the genus Burkholderia, a diverse group that is widespread across different environments and whose members can be mutualistic or pathogenic to plants, fungi, and animals. Burkholderia symbionts provide nutritional benefits and resistance against insecticides to stinkbugs, defend Lagria beetle eggs against pathogenic fungi, and may be involved in nitrogen metabolism in ants. In contrast to many other insect symbioses, the known associations with Burkholderia are characterized by environmental symbiont acquisition or mixed-mode transmission, resulting in interesting ecological and evolutionary dynamics of symbiont strain composition. Insect– Burkholderia symbioses present valuable model systems from which to derive insights into general principles governing symbiotic interactions because they are often experimentally and genetically tractable and span a large fraction of the diversity of functions, localizations, and transmission routes represented in insect symbioses.

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.

Seed Shape Diversity in families of the Order Ranunculales

Phytotaxa ◽  
2019 ◽  
Vol 425 (4) ◽  
pp. 193-207 ◽  
Author(s):  
JOSÈ JAVIER MARTÍN-GÓMEZ ◽  
AGNIESZKA REWICZ ◽  
EMILIO CERVANTES
Keyword(s):  
Arabidopsis Thaliana ◽  
Medicago Truncatula ◽  
Life Style ◽  
Lotus Japonicus ◽  
Seed Morphology ◽  
Life Cycles ◽  
Plant Structure ◽  
Seed Shape ◽  
The Third ◽  
Taxonomic Groups

Seed shape in the order Ranunculales is described with the objective of characterizing the morphological seed types in the families of this order and to establish a correlation between seed shape, plant structure and life style.         Based on previous work in model plants (Arabidopsis thaliana, Lotus japonicus, Medicago truncatula), we have used the J index to estimate the percentage of similarity of the image of a seed with a geometric shape. The images of seeds of model plants resemble cardioid or cardioid-derived models, while seeds from other species with rapid life cycles resemble other, also simple geometrical figures. In general, seed shape may help establishing the relationships between taxonomic groups.         Three types of seed morphology are distinguished in the Ranunculales based on values of J index. In the first type, seeds in the Berberidaceae, Euptelaceae and Lardizabalaceae, adjust well to an oval. The second type, seeds in the Papaveraceae, adjust well to the cardioid model, and the third type, seeds in the Ranunculaceae, adjust well to diverse geometric shapes, including the oval, truncated cardioid, Fibonacci spiral and ellipse. In the Ranunculales, seed shape is varied and often related to geometrical figures.                The presence of cardioid derived models in the Papaveraceae supports our hypothesis that seeds resembling the cardioid are frequent in plants with rapid life cycles.Ranunculales

scholarly journals Symbiotic signalling is at the core of an endophytic Fusarium solani-legume association

2019 ◽  
Author(s):  
Skiada Vasiliki ◽  
Marianna Avramidou ◽  
Paola Bonfante ◽  
Andrea Genre ◽  
Kalliope K. Papadopoulou
Keyword(s):  
Fusarium Solani ◽  
Lotus Japonicus ◽  
Arbuscular Mycorrhizal ◽  
Sensu Stricto ◽  
Root Penetration ◽  
Dependent Manner ◽  
Nuclear Calcium ◽  
Symbiotic Interactions ◽  
Wide Range ◽  
Calcium Spiking

AbstractLegumes interact with a wide range of microbes in their root system, ranging from beneficial symbionts to pathogens. Symbiotic rhizobia and arbuscular mycorrhizal glomeromycetes trigger a so-called common symbiotic signalling pathway (CSSP), including the induction of nuclear calcium spiking in the root epidermis. In our study, the recognition of an endophytic Fusarium solani strain K in Lotus japonicus induced the expression of LysM receptors for chitin-based molecules, CSSP members and CSSP-dependent genes in L. japonicus. In LysM and CSSP mutant/RNAi lines, root penetration and fungal intraradical progression was either stimulated or limited while FsK exudates are perceived in a CSSP-dependent manner, triggering nuclear calcium spiking in epidermal cells of Medicago truncatula Root Organ Cultures. Our results corroborate that the CSSP is a more common pathway than previously envisaged, involved in the perception of signals from other microbes beyond the restricted group of symbiotic interactions sensu stricto.

scholarly journals Establishment of Proximity-dependent Biotinylation Approaches in Different Plant Model Systems

2019 ◽  
Author(s):  
Deepanksha Arora ◽  
Nikolaj B. Abel ◽  
Chen Liu ◽  
Petra Van Damme ◽  
Klaas Yperman ◽  
...  
Keyword(s):  
Structural Information ◽  
Protein Complexes ◽  
Affinity Purification ◽  
Lotus Japonicus ◽  
Model Systems ◽  
Test Case ◽  
Plant Model ◽  
One Step ◽  
Subsequent Capture ◽  
Biotin Labelling

AbstractProximity-dependent biotin labelling (PDL) uses a promiscuous biotin ligase (PBL) or a peroxidase fused to a protein of interest. This enables covalent biotin labelling of proteins and allows subsequent capture and identification of interacting and neighbouring proteins without the need for the protein complex to remain intact. To date, only few papers report on the use of PDL in plants. Here we present the results of a systematic study applying a variety of PDL approaches in several plant systems using various conditions and bait proteins. We show that TurboID is the most promiscuous variant in several plant model systems and establish protocols which combine Mass Spectrometry-based analysis with harsh extraction and washing conditions. We demonstrate the applicability of TurboID in capturing membrane-associated protein interactomes using Lotus japonicus symbiotically active receptor kinases as test-case. We further benchmark the efficiency of various PBLs in comparison with one-step affinity purification approaches. We identified both known as well as novel interactors of the endocytic TPLATE complex. We furthermore present a straightforward strategy to identify both non-biotinylated as well as biotinylated peptides in a single experimental setup. Finally, we provide initial evidence that our approach has the potential to infer structural information of protein complexes.

scholarly journals Reflections on the Use of an Invertebrate Chordate Model System for Studies of Gut Microbial Immune Interactions

2021 ◽  
Vol 12 ◽  
Author(s):  
Assunta Liberti ◽  
Ojas Natarajan ◽  
Celine Grace F. Atkinson ◽  
Paolo Sordino ◽  
Larry J. Dishaw
Keyword(s):  
Innate Immunity ◽  
Marine Invertebrate ◽  
Model System ◽  
Model Systems ◽  
Functional Ecology ◽  
Immune Effector ◽  
Symbiotic Interactions ◽  
Computational Sciences ◽  
Primary Focus ◽  
Full Utilization

The functional ecology of the gastrointestinal tract impacts host physiology, and its dysregulation is at the center of various diseases. The immune system, and specifically innate immunity, plays a fundamental role in modulating the interface of host and microbes in the gut. While humans remain a primary focus of research in this field, the use of diverse model systems help inform us of the fundamental principles legislating homeostasis in the gut. Invertebrates, which lack vertebrate-style adaptive immunity, can help define conserved features of innate immunity that shape the gut ecosystem. In this context, we previously proposed the use of a marine invertebrate, the protochordate Ciona robusta, as a novel tractable model system for studies of host-microbiome interactions. Significant progress, reviewed herein, has been made to fulfill that vision. We examine and review discoveries from Ciona that include roles for a secreted immune effector interacting with elements of the microbiota, as well as chitin-rich mucus lining the gut epithelium, the gut-associated microbiome of adults, and the establishment of a large catalog of cultured isolates with which juveniles can be colonized. Also discussed is the establishment of methods to rear the animals germ-free, an essential technology for dissecting the symbiotic interactions at play. As the foundation is now set to extend these studies into the future, broadening our comprehension of how host effectors shape the ecology of these microbial communities in ways that establish and maintain homeostasis will require full utilization of “multi-omics” approaches to merge computational sciences, modeling, and experimental biology in hypothesis-driven investigations.

scholarly journals Newly established gastrointestinal cancer cell lines retain the genomic and immunophenotypic landscape of their parental cancers

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Daniela Hirsch ◽  
Steffen Seyfried ◽  
Tobias Staib ◽  
David Fiedler ◽  
Christian Sauer ◽  
...  
Keyword(s):  
Cell Lines ◽  
Cancer Cell ◽  
Molecular Mechanisms ◽  
Human Cancer ◽  
Cancer Cell Lines ◽  
Biological Properties ◽  
Model Systems ◽  
Comparative Genomic ◽  
Parental Tumor ◽  
Tumor Entities

Abstract Human cancer cell lines are frequently used as model systems to study molecular mechanisms and genetic changes in cancer. However, the model is repeatedly criticized for its lack of proximity to original patient tumors. Therefore, understanding to what extent cell lines cultured under artificial conditions reflect the phenotypic and genomic profiles of their corresponding parental tumors is crucial when analyzing their biological properties. To directly compare molecular alterations between patient tumors and derived cell lines, we have established new cancer cell lines from four patients with gastrointestinal tumors. Tumor entities comprised esophageal cancer, colon cancer, rectal cancer and pancreatic cancer. Phenotype and genotype of both patient tumors and derived low-passage cell lines were characterized by immunohistochemistry (22 different antibodies), array-based comparative genomic hybridization and targeted next generation sequencing (48-gene panel). The immunophenotype was highly consistent between patient tumors and derived cell lines; the expression of most markers in cell lines was concordant with the respective parental tumor and characteristic for the respective tumor entities in general. The chromosomal aberration patterns of the parental tumors were largely maintained in the cell lines and the distribution of gains and losses was typical for the respective cancer entity, despite a few distinct differences. Cancer gene mutations (e.g., KRAS, TP53) and microsatellite status were also preserved in the respective cell line derivates. In conclusion, the four examined newly established cell lines exhibited a phenotype and genotype closely recapitulating their parental tumor. Hence, newly established cancer cell lines may be useful models for further pharmacogenomic studies.

scholarly journals Rediscovering a Forgotten System of Symbiosis: Historical Perspective and Future Potential

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1063
Author(s):  
Vincent G. Martinson
Keyword(s):  
Historical Perspective ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Model Systems ◽  
Recent Common Ancestor ◽  
Comparative Genomic ◽  
Human Populations ◽  
Candida Auris ◽  
Most Recent Common Ancestor ◽  
Recent Emergence

While the majority of symbiosis research is focused on bacteria, microbial eukaryotes play important roles in the microbiota and as pathogens, especially the incredibly diverse Fungi kingdom. The recent emergence of widespread pathogens in wildlife (bats, amphibians, snakes) and multidrug-resistant opportunists in human populations (Candida auris) has highlighted the importance of better understanding animal–fungus interactions. Regardless of their prominence there are few animal–fungus symbiosis models, but modern technological advances are allowing researchers to utilize novel organisms and systems. Here, I review a forgotten system of animal–fungus interactions: the beetle–fungus symbioses of Drugstore and Cigarette beetles with their symbiont Symbiotaphrina. As pioneering systems for the study of mutualistic symbioses, they were heavily researched between 1920 and 1970, but have received only sporadic attention in the past 40 years. Several features make them unique research organisms, including (1) the symbiont is both extracellular and intracellular during the life cycle of the host, and (2) both beetle and fungus can be cultured in isolation. Specifically, fungal symbionts intracellularly infect cells in the larval and adult beetle gut, while accessory glands in adult females harbor extracellular fungi. In this way, research on the microbiota, pathogenesis/infection, and mutualism can be performed. Furthermore, these beetles are economically important stored-product pests found worldwide. In addition to providing a historical perspective of the research undertaken and an overview of beetle biology and their symbiosis with Symbiotaphrina, I performed two analyses on publicly available genomic data. First, in a preliminary comparative genomic analysis of the fungal symbionts, I found striking differences in the pathways for the biosynthesis of two B vitamins important for the host beetle, thiamine and biotin. Second, I estimated the most recent common ancestor for Drugstore and Cigarette beetles at 8.8–13.5 Mya using sequence divergence (CO1 gene). Together, these analyses demonstrate that modern methods and data (genomics, transcriptomes, etc.) have great potential to transform these beetle–fungus systems into model systems again.

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