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

文献类型： 外文期刊

作者： Liu, Ningyawen 1 ; Zhang, Lu 3 ; Zhou, Yanli 1 ; Tu, Mengling 2 ; Wu, Zhenzhen 1 ; Gui, Daping 1 ; Ma, Yongpeng 6 ; Wang, 1 ;

作者机构： 1.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China

2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China

3.Yunnan Acad Agr Sci, Flower Res Inst, Kunming 650205, Yunnan, Peoples R China

4.Natl Engn Res Ctr Ornamental Hort, Kunming 650205, Yunnan, Peoples R China

5.Chinese Acad Sci, Kunming Inst Bot, Yunnan Key Lab Wild Plant Resources, Key Lab Econ Plants & Biotechnol, Kunming 650201, Yunnan, Peoples R China

6.Chinese Acad Sci, Kunming Inst Bot, Yunnan Key Lab Integrat Conservat Plant Species E, Kunming 650201, Yunnan, Peoples R China

7.Chinese Acad Sci, Kunming Inst Bot, Haiyan Engn & Technol Ctr, Jiaxing 314300, Peoples R China

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

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2021 年 22 卷 1 期

页码：

收录情况： SCI

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.

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