The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron
| Autor: | Yan-Li Zhou, Zhenzhen Wu, Yongpeng Ma, Zhang Lu, Chengjun Zhang, Mengling Tu, Daping Gui, Ningyawen Liu, Ji-Hua Wang |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Rhododendron
Genomics QH426-470 Biology computer.software_genre Proteomics Genome Database 03 medical and health sciences 0302 clinical medicine Databases Genetic Genetics Humans Horticulture plant 030304 developmental biology Synteny Whole genome sequencing 0303 health sciences Functional genomics Plants Microsatellite DNA microarray Transcriptome computer TP248.13-248.65 030217 neurology & neurosurgery Genome Plant Biotechnology |
| Zdroj: | BMC Genomics BMC Genomics, Vol 22, Iss 1, Pp 1-10 (2021) |
| ISSN: | 1471-2164 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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