Ningyawen Liu1,2, Lu Zhang3,4, Yanli Zhou1, Mengling Tu2,5, Zhenzhen Wu1,2, Daping Gui1, Yongpeng Ma6, Jihua Wang7,8, Chengjun Zhang9,10. 1. Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. 2. University of Chinese Academy of Sciences, Beijing, 100049, China. 3. The Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China. 4. National Engineering Research Center for Ornamental Horticulture, Kunming, 650205, China. 5. Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. 6. Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. 7. The Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China. wjh0505@gmail.com. 8. National Engineering Research Center for Ornamental Horticulture, Kunming, 650205, China. wjh0505@gmail.com. 9. Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. zhangchengjun@mail.kib.ac.cn. 10. Haiyan Engineering & Technology Center, Kunming Institute of Botany, Chinese Academy of Sciences, Jiaxing, 314300, China. zhangchengjun@mail.kib.ac.cn.
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.
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.
Authors: Valerie L Soza; Dale Lindsley; Adam Waalkes; Elizabeth Ramage; Rupali P Patwardhan; Joshua N Burton; Andrew Adey; Akash Kumar; Ruolan Qiu; Jay Shendure; Benjamin Hall Journal: Genome Biol Evol Date: 2019-12-01 Impact factor: 3.416