The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron

• Main Authors: Ningyawen Liu, Lu Zhang, Yanli Zhou, Mengling Tu, Zhenzhen Wu, Daping Gui, Yongpeng Ma, Jihua Wang, Chengjun Zhang
• Format: Article
• Language: English
• Published: BMC 2021-05-01
• Series: BMC Genomics
• Subjects: Rhododendron; Horticulture plant; Database; Functional genomics
• Online Access: https://doi.org/10.1186/s12864-021-07704-0

Abstract Background The genus Rhododendron L. has been widely cultivated for hundreds of years around the world. Members of this genus are known for great ornamental and medicinal value. Owing to advances in sequencing technology, genomes and transcriptomes of members of the Rhododendron genus have been sequenced and published by various laboratories. With increasing amounts of omics data available, a centralized platform is necessary for effective storage, analysis, and integration of these large-scale datasets to ensure consistency, independence, and maintainability. Results Here, we report our development of the Rhododendron Plant Genome Database (RPGD; http://bioinfor.kib.ac.cn/RPGD/ ), which represents the first comprehensive database of Rhododendron genomics information. It includes large amounts of omics data, including genome sequence assemblies for R. delavayi, R. williamsianum, and R. simsii, gene expression profiles derived from public RNA-Seq data, functional annotations, gene families, transcription factor identification, gene homology, simple sequence repeats, and chloroplast genome. Additionally, many useful tools, including BLAST, JBrowse, Orthologous Groups, Genome Synteny Browser, Flanking Sequence Finder, Expression Heatmap, and Batch Download were integrated into the platform. Conclusions RPGD is designed to be a comprehensive and helpful platform for all Rhododendron researchers. Believe that RPGD will be an indispensable hub for Rhododendron studies.