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 are 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, 7 541 transmembrane (TM) proteins were predicted in the soybean genome, out of these, 3 306 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/.

中文翻译：

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大豆转运蛋白数据库 (SoyTD)：用于鉴定和探索大豆转运蛋白基因天然变异的综合数据库

转运蛋白是一类有助于跨细胞膜交换溶质（包括各种分子和离子）的膜蛋白，是所有生物体生存的重要组成部分。了解植物转运蛋白对于了解基本的细胞过程、生理学和分子机制非常重要，包括营养吸收、信号传导、对外部压力的反应等等。在这方面，对大豆和其他植物物种中预测的转运蛋白进行了广泛分析。此外，还开发了大豆转运蛋白综合数据库 SoyTD，通过整合表达、基因本体、保守域和基序，促进转运蛋白的识别、分类和广泛表征，基因结构组织和染色体分布特征。通过集成各种预测工具，进行了综合分析以识别高度可信的转运蛋白。最初，在大豆基因组中预测了 7 541 个跨膜 (TM) 蛋白，其中，选择了 3 306 个携带两个或多个跨膜结构域的非冗余转运蛋白基因进行进一步分析。根据标准转运蛋白分类（TC）系统对鉴定的转运蛋白基因进行分类。对 47 个植物基因组中转运蛋白基因的比较分析提供了对陆地植物转运蛋白基因扩增和复制的见解。整合了大豆的全基因组重测序 (WGRS) 和组织特异性转录组数据集，以研究与感兴趣的转运蛋白相关的天然变异和表达谱。总体而言，SoyTD 提供了一个全面的界面来研究大豆转运蛋白的遗传和分子功能。SoyTD 可在 http://artemis.cyverse.org/soykb_dev/SoyTD/ 上公开获取。