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Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters
Zhenyan Miao1, Daofeng Li, Zhenhai Zhang
1State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.
BMC Genomics
|February 8, 2012
Summary
A new database, the Medicago truncatula transporter database (MTDB), systematically catalogs all known transporters in the model legume Medicago truncatula. This resource aids researchers in exploring transporter functions and gene expression, particularly under stress conditions.
Area of Science:
- * Plant genomics and molecular biology.
- * Functional genomics and bioinformatics.
- * Legume biology and crop improvement.
Background:
- * Medicago truncatula serves as a key model organism for legume genomic research, closely related to alfalfa.
- * Membrane transporters are crucial for nutrient uptake, waste removal, and environmental sensing in cells.
- * Previous research identified individual M. truncatula transporters, but a consolidated, systematic database was lacking.
Purpose of the Study:
- * To develop and present a comprehensive, systematic database for all M. truncatula transporters.
- * To provide a centralized resource for exploring transporter annotations, functions, and expression patterns.
- * To facilitate comparative analysis and functional studies of M. truncatula transporters.
Main Methods:
- * Utilized the TransportTP method for a novel transporter prediction pipeline.
- * Annotated 3,665 putative M. truncatula transporters based on IMGAG V3.5 and MTGI V10.0.
- * Classified transporters into 162 families and seven types based on transport mode and energy coupling.
- * Generated extensive annotations including protein function, EST mapping, genome locus, and structural predictions.
- * Developed a chromosome distribution map and BLAST tools, with options to explore stress-induced gene expression.
Main Results:
- * Established the Medicago truncatula transporter database (MTDB) with 3,665 putative transporters.
- * Classified transporters into 162 families and seven functional types.
- * Provided detailed annotations and tools for exploring transporter characteristics and chromosomal distribution.
- * Enabled investigation of transporter gene expression under stress conditions.
Conclusions:
- * The MTDB offers a valuable platform for exploring and comparing M. truncatula transporters.
- * Its user-friendly web interface and regular updates support researchers in related fields.
- * The MTDB is freely accessible for advancing legume research and functional genomics.
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