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The Genome Database for Rosaceae (GDR): year 10 update

Sook Jung, Stephen P. Ficklin, Taein Lee, Chun-Huai Cheng, Anna Blenda, Ping Zheng, Jing Yu, Aureliano Bombarely, Ilhyung Cho, Sushan Ru, Kate Evans, Cameron Peace (+4 others)
2013 Nucleic Acids Research  
The Genome Database for Rosaceae (GDR, http:/ www.rosaceae.org), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding  ...  New expressed sequence tag unigene sets are available for major genera, and Pathway data are available through FragariaCyc, AppleCyc and PeachCyc databases.  ...  ACKNOWLEDGEMENTS The authors thank their funding sources, the Rosaceae research community for providing data and feedback and the Tripal community of developers for developing and sharing Tripal modules  ... 
doi:10.1093/nar/gkt1012 pmid:24225320 pmcid:PMC3965003 fatcat:rkn52cq5avdjxlafga3l5o57aq

15 years of GDR: New data and functionality in the Genome Database for Rosaceae

Sook Jung, Taein Lee, Chun-Huai Cheng, Katheryn Buble, Ping Zheng, Jing Yu, Jodi Humann, Stephen P Ficklin, Ksenija Gasic, Kristin Scott, Morgan Frank, Sushan Ru (+11 others)
2018 Nucleic Acids Research  
The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining  ...  The volume of data in GDR has increased greatly over the last 5 years.  ...  ACKNOWLEDGEMENTS The authors acknowledge with thanks their funding sources, the Rosaceae research community for providing data, support and feedback, the Tripal and GMOD community of developers for developing  ... 
doi:10.1093/nar/gky1000 pmid:30357347 pmcid:PMC6324069 fatcat:mwwos4ljmnekvl4u6penvw2joa

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases

Margaret Staton, Ethalinda Cannon, Lacey-Anne Sanderson, Jill Wegrzyn, Tavis Anderson, Sean Buehler, Irene Cobo-Simón, Kay Faaberg, Emily Grau, Valentin Guignon, Jessica Gunoskey, Blake Inderski (+8 others)
2021 Briefings in Bioinformatics  
With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing  ...  databases, and support for implementing FAIR principles.  ...  The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.  ... 
doi:10.1093/bib/bbab238 pmid:34251419 pmcid:PMC8574961 fatcat:khqsm7dedrgupeu7h5iyaoi7wi

An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals

Muzi Li, Yuwei Xiao, Steve Mount, Zhongchi Liu
2021 Frontiers in Plant Science  
This review summarizes major genomic resources and genome research progress in Rosaceae, highlights important databases, and suggests areas for further improvement.  ...  Additionally, due to the diversity of fruit types in Rosaceae, this plant family offers excellent opportunities for investigations into fleshy fruit diversity, evolution, and development.  ...  Rosaceae Genome Databases Genome Database for Rosaceae (GDR) (www.rosaceae.org) (Jung et al., 2019) is, by far, the best resource hub for Rosaceae research.  ... 
doi:10.3389/fpls.2021.644881 pmid:33868343 pmcid:PMC8047320 fatcat:hd2zdeh565cc3iq3czl6zywt4a

Genomics and bioinformatics resources for translational science in Rosaceae

Sook Jung, Dorrie Main
2013 Plant Biotechnology Reports  
This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.  ...  Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data.  ...  Nucleic Acids Research Database Addition published every January.Recently, several genomes of Rosaceae have been sequenced and some of these are available from the Genome Database for Rosaceae (GDR, http  ... 
doi:10.1007/s11816-013-0282-3 pmid:24634697 pmcid:PMC3951882 fatcat:4jygw6x3enas7bhe4yic7m76ou

RIGD: A Database for Intronless Genes in the Rosaceae

Tianzhe Chen, Dandan Meng, Xin Liu, Xi Cheng, Han Wang, Qing Jin, Xiaoyu Xu, Yunpeng Cao, Yongping Cai
2020 Frontiers in Genetics  
Due to the absence of introns, intronless genes in eukaryotes have become important materials for comparative genomics and evolutionary biology.  ...  In this study, we constructed the Rosaceae Intronless Genes Database (RIGD), a user-friendly web interface to explore and collect information on intronless genes from different plants.  ...  The funders had no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.  ... 
doi:10.3389/fgene.2020.00868 pmid:32849839 pmcid:PMC7426402 fatcat:uapn3plynrcsbmvpbgtx3er5gm

Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment

Jill L. Wegrzyn, Margaret A. Staton, Nathaniel R. Street, Dorrie Main, Emily Grau, Nic Herndon, Sean Buehler, Taylor Falk, Sumaira Zaman, Risharde Ramnath, Peter Richter, Lang Sun (+6 others)
2019 Frontiers in Plant Science  
They provide frameworks to view and update annotations for complex genomes, interrogate systems level expression profiles, curate data for comparative genomics, and perform real-time analysis with genotype  ...  The tree databases reviewed here serve as secondary repositories for community data.  ...  GENOME DATABASE FOR ROSACEAE The Genome Database for Rosaceae (GDR 2 , Jung et al., 2013) was initiated in 2003 to provide curated and integrated, genomic, genetics and breeding (GGB) data alongside  ... 
doi:10.3389/fpls.2019.00813 pmid:31293610 pmcid:PMC6603172 fatcat:vpbwpe3sg5f3hmnzboiwaxanga

Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado

Sook Jung, Taein Lee, Stephen Ficklin, Jing Yu, Chun-Huai Cheng, Dorrie Main
2016 Database: The Journal of Biological Databases and Curation  
The Genome Database for Rosaceae (GDR) and CottonGen are comprehensive online data repositories that provide access to integrated genomic, genetic and breeding data through search, visualization and analysis  ...  Database URL: GDR (www.rosaceae.org), CottonGen (www.cottongen.org) V C The Author(s)  ...  The Genome Database for Rosaceae (GDR) and CottonGen are (25) one of the first, if not the only, databases that adopted Chado/Tripal solely to store integrated genetic, genomic and breeding data comprised  ... 
doi:10.1093/database/baw010 pmid:26989146 pmcid:PMC4795932 fatcat:ulmoo7j3gvhync3j3lipxvbtgq

Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado

Sook Jung, Taein Lee, Stephen Ficklin, Jing Yu, Chun-Huai Cheng, Dorrie Main
2016 Database: The Journal of Biological Databases and Curation  
The Genome Database for Rosaceae (GDR) and CottonGen are comprehensive online data repositories that provide access to integrated genomic, genetic and breeding data through search, visualization and analysis  ...  These online databases use Chado, an open-source, generic and ontology-driven database schema for biological data, as the primary data storage platform.  ...  The Genome Database for Rosaceae (GDR) and CottonGen are (25) one of the first, if not the only, databases that adopted Chado/Tripal solely to store integrated genetic, genomic and breeding data comprised  ... 
doi:10.1093/database/baw058 pmid:27141090 pmcid:PMC4852396 fatcat:ag5724tx6ndezh3qhs45l5eom4

The Sequenced Angiosperm Genomes and Genome Databases

Fei Chen, Wei Dong, Jiawei Zhang, Xinyue Guo, Junhao Chen, Zhengjia Wang, Zhenguo Lin, Haibao Tang, Liangsheng Zhang
2018 Frontiers in Plant Science  
The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major  ...  Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including  ...  Fujian Agriculture and Forestry University to LZ, and FC is supported by a grant from State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops (SKB2017004).  ... 
doi:10.3389/fpls.2018.00418 pmid:29706973 pmcid:PMC5909171 fatcat:v5av6eiadrgw5lmt2qmzqlesrq

Version VI of the ESTree db: an improved tool for peach transcriptome analysis

Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Ivan Merelli, Francesca Barale, Luciano Milanesi, Alessandra Stella, Carlo Pozzi
2008 BMC Bioinformatics  
Apart from standard clustering and annotation analyses, version VI of the ESTree db encompasses new tools for tandem repeat identification, annotation against genomic Rosaceae sequences, and positioning  ...  Flexibility and modularity of the ESTree analysis pipeline and of the web interface allowed the authors to set up similar structures for different datasets, with limited manual intervention.  ...  Gary Barker for providing the AutoSNP program, Dr Alberto Montironi for preparing the program for automatic BIN assignment, Dr. Massoud Malek for help with the informatics work and Prof.  ... 
doi:10.1186/1471-2105-9-s2-s9 pmid:18387211 pmcid:PMC2323672 fatcat:y4lpynxaancizpayoxkzilyxku

PeachVar-DB: A Curated Collection of Genetic Variations for the Interactive Analysis of Peach Genome Data

Marco Cirilli, Tiziano Flati, Silvia Gioiosa, Ilario Tagliaferri, Angelo Ciacciulli, Zhongshan Gao, Stefano Gattolin, Filippo Geuna, Francesco Maggi, Paolo Bottoni, Laura Rossini, Daniele Bassi (+2 others)
2017 Plant and Cell Physiology  
PeachVar-DB results are linked to the Genome Database for Rosaceae (GDR) and the Phytozome database to allow easy access to other external useful plant-oriented resources.  ...  We designed a user-friendly webbased interface of the database, providing search tools to retrieve single nucleotide polymorphism (SNP) and InDel variants, along with useful statistics and information.  ...  Antonella Pintus for constructive criticism of the manuscript and also would like to thank the LISA initiative 2016-2018 [http://www.hpc.cineca. it/content/lisa-call] and the Italian Node of Elixir project  ... 
doi:10.1093/pcp/pcx183 pmid:29216377 fatcat:5i5vong66ngqzotgtktgs4m3hy

Genomics of pear and other Rosaceae fruit trees

Toshiya Yamamoto, Shingo Terakami
2016 Breeding Science  
Genome Database for the Rosaceae (GDR; http://www.rosaceae.org).  ...  In recent years, international collaborative studies by the Rosaceae research community have hastened progress in developing genetic and genomic resources for representa tive crops such as apple (M. ×  ... 
doi:10.1270/jsbbs.66.148 pmid:27069399 pmcid:PMC4780798 fatcat:oeshtsjvd5em3dxlhihozqihcu

Prunus genetics and applications after de novo genome sequencing: achievements and prospects

Maria José Aranzana, Véronique Decroocq, Elisabeth Dirlewanger, Iban Eduardo, Zhong Shan Gao, Ksenija Gasic, Amy Iezzoni, Sook Jung, Cameron Peace, Humberto Prieto, Ryutaro Tao, Ignazio Verde (+2 others)
2019 Horticulture Research  
Finally, we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae (GDR) and its updated functionalities for future bioinformatics-based  ...  Within the structural and evolutionary contexts, we summarize: (1) the current status of Prunus whole-genome sequences; (2) preliminary and ongoing work on the sequence structure and diversity of the genomes  ...  Acknowledgements This research was supported in part by grants from the Ministry of Economy and Competitiveness (MINECO/FEDER projects AGL2015-68329-R and RTA2015-00050-00-00, Severo Ochoa Program for  ... 
doi:10.1038/s41438-019-0140-8 pmid:30962943 pmcid:PMC6450939 fatcat:tyznhjvbnbeflopfnv76zlihcu

GDS: A Genomic Database for Strawberries (Fragaria spp.)

Yuhan Zhou, Yushan Qiao, Zhiyou Ni, Jianke Du, Jinsong Xiong, Zongming Cheng, Fei Chen
2021 Horticulturae  
To promote the reuse and exploration of strawberry genomic data and enable extensive analyses using various bioinformatics tools, we have developed the Genome Database for Strawberry (GDS).  ...  Strawberry species (Fragaria spp.) are known as the "queen of fruits" and are cultivated around the world. Over the past few years, eight strawberry genome sequences have been released.  ...  We thank Xiaogang Lei and Xiaojiang Li for providing technical assistance to our database development and Fei Chen, Zongming Cheng for assistance with the correction of the English language in the manuscript  ... 
doi:10.3390/horticulturae8010041 fatcat:fnd4enrkfbfzdpbultr5v5naty
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