Deshmukh, R and Rana, N and Liu, Y and Zeng, S and Agarwal, G and Sonah, H and Varshney, R K and Joshi, T and Patil, G B and Nguyen, H T (2020) Soybean transporter database: A comprehensive database for identification and exploration of natural variants in soybean transporter genes. Physiologia Plantarum (TSI), 171 (4). pp. 756-770. ISSN 0031-9317
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Abstract
Transporters, a class of membrane proteins that facilitate exchange of solutes including diverse molecules and ions across the cellular membrane, are vital component for the survival of all organisms. Understanding plant transporters is important to get insight of the basic cellular processes, physiology, and molecular mechanisms including nutrient uptake, signaling, response to external stress, and many more. In this regard, extensive analysis of transporters predicted in soybean and other plant species was performed. In addition, an integrated database for soybean transporter protein, SoyTD, was developed that will facilitate the identification, classification, and extensive characterization of transporter proteins by integrating expression, gene ontology, conserved domain and motifs, gene structure organization, and chromosomal distribution features. A comprehensive analysis was performed to identify highly confident transporters by integrating various prediction tools. Initially, 7541 transmembrane (TM) proteins were predicted in the soybean genome; out of these, 3306 non-redundant transporter genes carrying two or more transmembrane domains were selected for further analysis. The identified transporter genes were classified according to a standard transporter classification (TC) system. Comparative analysis of transporter genes among 47 plant genomes provided insights into expansion and duplication of transporter genes in land plants. The whole genome resequencing (WGRS) and tissue-specific transcriptome datasets of soybean were integrated to investigate the natural variants and expression profile associated with transporter(s) of interest. Overall, SoyTD provides a comprehensive interface to study genetic and molecular function of soybean transporters. SoyTD is publicly available at http://artemis.cyverse.org/soykb_dev/SoyTD/.
| Item Type: | Article |
|---|---|
| Divisions: | Center of Excellence in Genomics and Systems Biology |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | soybean, plant transporters, physiology |
| Subjects: | Others > Crop Physiology Others > Genetics and Genomics |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 17 Apr 2025 03:28 |
| Last Modified: | 17 Apr 2025 03:28 |
| URI: | http://oar.icrisat.org/id/eprint/13035 |
| Official URL: | https://onlinelibrary.wiley.com/doi/epdf/10.1111/p... |
| Projects: | UNSPECIFIED |
| Funders: | Government of India - Department of Biotechnology, State of Texas' Governor's University Research Initiative, United Soybean Board |
| Acknowledgement: | The authors are thankful to the Department of Biotechnology, Government of India, for the Ramalingaswami Fellowship Award to RD and HS; United States Soybean Board for funding support to HN and State of Texas' Governor's University Research Initiative (GURI) support to GBP. |
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