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Genome Annotation
Annotation of Mtr 3.0 pseudomolecules by the International Medicago Genome Annotation Group (IMGAG), searchable by key word, gene identifier or chromosomal location can be found here. Sets of predicted coding sequences and proteins are available for blast searching and downloading. The IMGAG annotation pipeline uses the EuGene prediction pipeline and is run on each new pseudomolecule build and thus will not contain annotation for the most recent BACs in GenBank.
ESTs
All publicly available M. truncatula ESTs as well as transcripts from GenBank have been assembled into contigs as part of the TIGR Plant Transcript Assemblies. The Medicago truncatula Gene Index (MtGI) is now hosted at the Dana Faber Cancer Center.
BAC Ends
Medicago BAC ends have been sequenced by the following groups/institutions: TIGR, INRA/Genoscope, JIC/Sanger Center, Agricultural Biotechnology Center, Hungary, The Crop Biotechnology Center, Texas A&M University, Department of Plant Pathology, University of Minnesota. Files of all publicly available BAC ends can be downloaded from our FTP site.
Microarrays
The Affymetrix GeneChip® Medicago Genome Array is designed specifically to monitor gene expression in Medicago truncatula, Medicago sativa, and the symbiotic organism Sinorhizobium meliloti. The tables/database contains all probes and their corresponding targets, gene ids are linked to the TIGR Medicago Gene Index TCs/ests, IMGAG genes and TIGR Sinorhizobium meliloti CMR. A mapping of the probesets to the IMGAG-annotated Mtr 2.0 pseudomolecules can be found here. A 16K long oligonucleotide set for spotted arrays was developed in collaboration with Operon based upon MtGI 5.0. The probe set was later mapped to MtGI Release 8.0 (Threshold 98.5 %ID 90% coverage). SLIM GO annotation was performed by mapping to the TAIR Arabidopsis assignments (threshold e-10, from a database size of 119546). Over 13000 probes/TCs were assigned a SLIM GO annotation.
Repeat Databases
A comprehensive database of M. truncatula repeats has been generated by IMGAG during the course of genome annotation using a combination of de novo repeats detected by RepeatScout and known and curated repeats and transposons from GenBank and is available for download. An earlier repeat database constructed by similarity to known repeat elements can be found as part of the TIGR Repeat Databases.
For Comments/Questions send mail to mtruncatula@jcvi.org.