Stimulation of alanine amino transferase (AlaAT) gene expression and alanine accumulation in embryo axis of the model legume Medicago truncatula contribute to anoxia stress tolerance

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.

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MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula

BMC Research Notes ◽

10.1186/1756-0500-3-262 ◽

2010 ◽

Vol 3 (1) ◽

Author(s):

Kolja Henckel ◽

Helge Küster ◽

Leonhard J Stutz ◽

Alexander Goesmann

Keyword(s):

Gene Expression ◽

Medicago Truncatula ◽

In Silico ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Model Legume

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

10.1101/2021.05.27.445921 ◽

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.

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Alternative oxidase 1 (Aox1) gene expression in roots of Medicago truncatula is a genotype-specific component of salt stress tolerance

Journal of Plant Physiology ◽

10.1016/j.jplph.2012.08.017 ◽

2013 ◽

Vol 170 (1) ◽

pp. 111-114 ◽

Cited By ~ 26

Author(s):

Haythem Mhadhbi ◽

Vasileios Fotopoulos ◽

Photini V. Mylona ◽

Moez Jebara ◽

Mohamed Elarbi Aouani ◽

...

Keyword(s):

Gene Expression ◽

Salt Stress ◽

Stress Tolerance ◽

Medicago Truncatula ◽

Alternative Oxidase ◽

Salt Stress Tolerance ◽

Specific Component

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Transcriptional snapshots provide insights into the molecular basis of arbuscular mycorrhiza in the model legume Medicago truncatula

Functional Plant Biology ◽

10.1071/fp06079 ◽

2006 ◽

Vol 33 (8) ◽

pp. 737 ◽

Cited By ~ 20

Author(s):

Natalija Hohnjec ◽

Kolja Henckel ◽

Thomas Bekel ◽

Jerome Gouzy ◽

Michael Dondrup ◽

...

Keyword(s):

Gene Expression ◽

Medicago Truncatula ◽

Mycorrhizal Fungi ◽

Molecular Basis ◽

Gene Expression Regulation ◽

Expressed Sequence Tag ◽

Marker Genes ◽

Plant Genomics ◽

Terrestrial Plants ◽

Model Legume

The arbuscular mycorrhizal (AM) association between terrestrial plants and soil fungi of the phylum Glomeromycota is the most widespread beneficial plant–microbe interaction on earth. In the course of the symbiosis, fungal hyphae colonise plant roots and supply limiting nutrients, in particular phosphorus, in exchange for carbon compounds. Owing to the obligate biotrophy of mycorrhizal fungi and the lack of genetic systems to study them, targeted molecular studies on AM symbioses proved to be difficult. With the emergence of plant genomics and the selection of suitable models, an application of untargeted expression profiling experiments became possible. In the model legume Medicago truncatula, high-throughput expressed sequence tag (EST)-sequencing in conjunction with in silico and experimental transcriptome profiling provided transcriptional snapshots that together defined the global genetic program activated during AM. Owing to an asynchronous development of the symbiosis, several hundred genes found to be activated during the symbiosis cannot be easily correlated with symbiotic structures, but the expression of selected genes has been extended to the cellular level to correlate gene expression with specific stages of AM development. These approaches identified marker genes for the AM symbiosis and provided the first insights into the molecular basis of gene expression regulation during AM.

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