Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis

被引:148
作者
Journet, EP [1 ]
van Tuinen, D
Gouzy, J
Crespeau, H
Carreau, V
Farmer, MJ
Niebel, A
Schiex, T
Jaillon, O
Chatagnier, O
Godiard, L
Micheli, F
Kahn, D
Gianinazzi-Pearson, V
Gamas, P
机构
[1] INRA, CNRS, Lab Biol Mol Relat Plantes Microorganismes, F-31326 Castanet Tolosan, France
[2] INRA, Lab Biometrie & Intelligence Artificielle, F-31326 Castanet Tolosan, France
[3] Univ Bourgogne, INRA, UMR Biochim 1088, F-21065 Dijon, France
[4] Genoscope, F-91057 Evry, France
[5] CNRS, UMR 8030, F-91057 Evry, France
关键词
D O I
10.1093/nar/gkf685
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:5579 / 5592
页数:14
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