The Lotus Transcript Profiling Resource

Introduction
  -  Methods
  -  Resource Description
  -  References
Probe set and Gene names
Visualization and Profile matching
Contrasts
Raw Data
Annotate



 Welcome!
to the Lotus japonicus transcript profiling resource. Below you will find an introduction to Lotus symbiotic biology as well as descriptions of all features of this site.

A legume model
Lotus japonicus is a wild perennial legume with a small diploid genome and a short lifecycle, and has been adopted as one of the principal model legumes. Legumes, which constitute the third largest family (Fabaceae) of flowering plants, are crucial crops and second only to grasses in their economic and nutritional importance. A key trait of legumes is the competence for symbiotic nitrogen fixation (SNF), which is the result of an intimate relationship with a group of soil living bacteria collectively called rhizobia. Initial signal exchange triggers a plant morphogenetic program leading to the formation of nodules on the root, inside which bacteria fix gaseous nitrogen into mineral nitrogen available to the plant, thus eliminating the need for nitrogen fertilisation. Not only does the comprehension of this mutualistic association hold the key to a better exploitation of a trait immensely important in agriculture, it also provides insights into molecular processes controlling microbe recognition, pathogen defense and plant organogenesis.

The goal of research in SNF is to identify and assign a function to all genes acting in the molecular signalling pathway leading from bacterial recognition to development of a new plant organ, the nodule, and to figure out how they interact. Legumes encode all functions necessary to develop a nodule, which is evident from the spontaneous nodulation seen in certain legume mutants grown in the absence of bacteria [1,2]. Thus, by studying plant genes alone, the genetic predisposition for SNF can be elucidated. In recent years, several key loci have been exposed, mainly based on map-based cloning approaches (reviewed in [3]), seeking to characterize symbiotic mutants impaired at different stages of nodulation.

As a result of large-scale genome sequencing efforts, however, lists of genes with unknown functions are expanding rapidly, and, consequently, there is a need to involve high-throughput approaches to be able to characterize genes more rapidly. For some time, functional genomics tools have been maturing in Arabidopsis research, and array-based transcript profiling has become efficient and widely used. One major outcome is the expansion of data resources, like the AtGenExpress project, that hold valuable information for almost any gene of interest.

However, in contrast to Arabidopsis, legumes are hosts to both endosymbiotic bacteria and mycorrhizal fungi, making them interesting in their own respect and essential to the understanding of these highly essential phenomena. Therefore, the recent availability of functional genomics tools to the legume community, immediately sparked several studies of rhizobial and mycorrhizal associations using EST-based macro- and micro-arrays in both Medicago truncatula [4,5] and Lotus [6-9], identifying several mycorrhiza-induced genes as well as inoculation-responsive genes (early nodulins) and genes functioning in the mature nodule (late nodulins). Non-nodulating mutants have also been studied using a 10K Medicago truncatula oligonucleotide array [10], and the feasibility of a rapid transcript-based cloning approach has been demonstrated [11].

The Lotus japonicus genome sequencing project has now allowed the design of an Affymetrix GeneChip® containing more than 52.000 Lotus probesets, representing all known and predicted open reading frames (ORFs). Here we present a web-accessible resource holding gene expression data covering several aspects of legume development and symbiotic biology.