The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron.
The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron.
复制标题
杜鹃花植物基因组数据库 (RPGD)：杜鹃花综合在线组学数据库
DOI：
10.1186/s12864-021-07704-0
复制
发表时间：
2021-05-22
期刊：
影响因子：
4.4
通讯作者：
Zhang C
中科院分区：
文献类型：
--
作者：
Liu N;Zhang L;Zhou Y;Tu M;Wu Z;Gui D;Ma Y;Wang J;Zhang C
背景
杜鹃花属Rhododendron L.已经在世界各地被广泛种植了数百年。本属的成员是已知的伟大的观赏和药用价值。由于测序技术的进步，杜鹃花属成员的基因组和转录组已被测序并由各个实验室发表。随着可用组学数据量的增加，集中式平台对于有效存储、分析和集成这些大规模数据集以确保一致性、独立性和可维护性是必要的。
结果
在此，我们报告了我们的杜鹃花植物基因组数据库（RPGD; http：//bioinfor.kib.ac.cn/RPGD/）的发展，这是第一个全面的杜鹃花基因组信息数据库。它包括大量的组学数据，包括R.德拉瓦伊河wildingsianum和R. Simsii，来自公开RNA-Seq数据的基因表达谱，功能注释，基因家族，转录因子鉴定，基因同源性，简单序列重复和叶绿体基因组。此外，许多有用的工具，包括BLAST，JBrowse，Orthogonal Groups，Genome Synteny Browser，Flanking Sequence Browser，Expression Heatmap和Batch Download都集成到该平台中。
结论
RPGD旨在为所有杜鹃花研究人员提供一个全面而有用的平台。相信RPGD将成为杜鹃花研究不可或缺的枢纽。
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.
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DOI：
10.1007/978-3-319-90698-0_11
发表时间：
2018-01-01
期刊：
ORNAMENTAL CROPS
影响因子：
--
作者：
De Riek, Jan;De Keyser, Ellen;Kobayashi, Nobuo
通讯作者：
Kobayashi, Nobuo
影响因子：
12.3
作者：
Buels R;Yao E;Diesh CM;Hayes RD;Munoz-Torres M;Helt G;Goodstein DM;Elsik CG;Lewis SE;Stein L;Holmes IH
通讯作者：
Holmes IH
影响因子：
10.7
作者：
Huerta-Cepas J;Forslund K;Coelho LP;Szklarczyk D;Jensen LJ;von Mering C;Bork P
通讯作者：
Bork P
影响因子：
14.9
作者：
Mitchell AL;Attwood TK;Babbitt PC;Blum M;Bork P;Bridge A;Brown SD;Chang HY;El-Gebali S;Fraser MI;Gough J;Haft DR;Huang H;Letunic I;Lopez R;Luciani A;Madeira F;Marchler-Bauer A;Mi H;Natale DA;Necci M;Nuka G;Orengo C;Pandurangan AP;Paysan-Lafosse T;Pesseat S;Potter SC;Qureshi MA;Rawlings ND;Redaschi N;Richardson LJ;Rivoire C;Salazar GA;Sangrador-Vegas A;Sigrist CJA;Sillitoe I;Sutton GG;Thanki N;Thomas PD;Tosatto SCE;Yong SY;Finn RD
通讯作者：
Finn RD
影响因子：
5.8
作者：
Deng, Wenjie;Nickle, David C.;Mullins, James I.
通讯作者：
Mullins, James I.