Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis.
We report on a large-scale expressed sequence tag (EST) sequencing and analysis program aimed at characterizing the sets of genes expressed in roots of the model legume Medicago truncatula during interactions with either of two microsymbionts, the nitrogen-fixing bacterium Sinorhizobium meliloti or the arbuscular mycorrhizal fungus Glomus intraradices. We have designed specific tools for in silico analysis of EST data, in relation to chimeric cDNA detection, EST clustering, encoded protein prediction, and detection of differential expression. Our 21 473 5'- and 3'-ESTs could be grouped into 6359 EST clusters, corresponding to distinct virtual genes, along with 52 498 other M.truncatula ESTs available in the dbEST (NCBI) database that were recruited in the process. These clusters were manually annotated, using a specifically developed annotation interface. Analysis of EST cluster distribution in various M.truncatula cDNA libraries, supported by a refined R test to evaluate statistical significance and by 'electronic northern' representation, enabled us to identify a large number of novel genes predicted to be up- or down-regulated during either symbiotic root interaction. These in silico analyses provide a first global view of the genetic programs for root symbioses in M.truncatula. A searchable database has been built and can be accessed through a public interface.
Journet
Etienne-Pascal
EP
Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, CNRS-INRA, Laboratoire de Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan Cedex, France. journet@toulouse.inra.fr
van Tuinen
Diederik
D
Gouzy
Jérome
J
Crespeau
Hervé
H
Carreau
Véronique
V
Farmer
Mary-Jo
MJ
Niebel
Andreas
A
Schiex
Thomas
T
Jaillon
Olivier
O
Chatagnier
Odile
O
Godiard
Laurence
L
Micheli
Fabienne
F
Kahn
Daniel
D
Gianinazzi-Pearson
Vivienne
V
Gamas
Pascal
P
D016000:Cluster Analysis; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D020224:Expressed Sequence Tags; D015966:Gene Expression Regulation, Fungal; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D029902:Medicago / Q000235:genetics* / Q000382:microbiology; D008969:Molecular Sequence Data; D038821:Mycorrhizae / Q000235:genetics / Q000254:growth & development; D018517:Plant Roots / Q000235:genetics* / Q000382:microbiology; D017422:Sequence Analysis, DNA; D013559:Symbiosis / Q000235:genetics*
D018076:DNA, Complementary