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

BMC Genomics

Yanli Zhou¹  Daping Gui¹  Chengjun Zhang²  Ningyawen Liu³  Zhenzhen Wu³  Lu Zhang⁴  Jihua Wang⁴  Mengling Tu⁵  Yongpeng Ma⁶ 

[1] Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China;Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China;Haiyan Engineering & Technology Center, Kunming Institute of Botany, Chinese Academy of Sciences, 314300, Jiaxing, China;Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China;University of Chinese Academy of Sciences, 100049, Beijing, China;The Flower Research Institute, Yunnan Academy of Agricultural Sciences, 650205, Kunming, China;National Engineering Research Center for Ornamental Horticulture, 650205, Kunming, China;University of Chinese Academy of Sciences, 100049, Beijing, China;Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China;Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China;

关键词: Rhododendron;    Horticulture plant;    Database;    Functional genomics;   

DOI  :  10.1186/s12864-021-07704-0

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsHere, 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.ConclusionsRPGD is designed to be a comprehensive and helpful platform for all Rhododendron researchers. Believe that RPGD will be an indispensable hub for Rhododendron studies.

【 授权许可】

CC BY