Soybean Transporter Database (SoyTD): Genome-Wide Identification and Exploration of Natural Variants in Soybean Transporter Genes

Transporter proteins are membrane channels/pumps which plays a key role in exchange of selective molecules and ions from the external or internal environment. We developed an integrated database for soybean membrane proteins, SoyTD that facilitates the interpretation of transporter genes and protein sequence data by integrating features that are available from individual sources. Using publically available prediction programs, putative integral membrane proteins were identified among the 56,044 proteins in the soybean genome (Wm82.a2.v1). The prediction from the transporter classification database (TCDB) identified approximately 7,541 proteins as transmembrane (TM) candidate proteins. Out of these, 3,306 non-redundant transporter genes containing at least two transmembrane domains were identified and classified according to the transporter classification (TC) system. Genome-wide comparative analysis of transporter genes in 49 plant genomes provided insights into the evolution, expansion and duplication of transporter genes in the land plants. Whole genome resequencing (WGRS) data and tissue specific transcriptome datasets of soybean were integrated to investigate the natural variants and expression profiles associated with transporter(s) of interest. Overall, the SoyTD (http://soykb.org/transporters/) provides a comprehensive interface to soybean researcher to study genetic and molecular function and, will aid as an important resource for soybean improvement.