Transcript Genome Database for Rosaceae: New Data and New

Genome Database for Rosaceae
New Data and New Functionality
Fruit and Nut Workshop
Plant and Animal Genome Conference 2017
Dorrie Main*, Sook Jung, Chun-Huai Cheng, Taein Lee, Ping Zheng,
Jing Yu, Jodi Humann, Kristin Scott, Morgan Frank, Heidi Haugh,
Cameron Peace, Kate Evans, Mike Kahn, Albert Abbott, Ksenija
Gasic, Mercy Olmstead, Michael Coe
*[email protected]
GDR Vision Part 1
Facilitate Rosaceae Research
• Discovery
• Translation
• Application
Made possible by
• A highly supportive and engaged community
• Continuous funding (2003-2019) from NSF PGRP, USDA SCRI,
Industry and Land Grant Universities
• An excellent development and curation team
The Team
GDR Vision Part 2
Develop open source software resources to
facilitate sharing of tools and data across
the bioinformatics community
CHADO
New Data in GDR in 2016
Data Type
01/01/16
01/01/17
Increase
Genes
150,815
242,182
91,367
Genomes
11
16
5
Genetic maps
160
180
20
Genotypes
28,298
15,513,927
15,485,631
Germplasm
16,345
18,642
2,297
Markers
2,311,771
2,900,018
588,247
Phenotypes
783,639
876,885
93,246
Publications
6,703
6,888
185
QTLs
2,318
2,695
377
Transcripts
0
60,716
60,716
New Functionality in 2016
• GDR redesigned to make it easier to access data and tools.
• Synteny analysis for peach-apple-strawberry-pear in
GBrowse_Sy
• RubusCyc database added and other Cycs updated
• Reference transcriptomes (RefTrans) for Rubus and peach
• New search interfaces developed
(1) SNP marker search (2) SNP genotype search
(3) Gene and transcript search (4) Map search
(5) Germplasm image search
• Dynamically generated data overview page implemented
• Crop Ontology developed and implemented for Rosaceae species
• 16 short audio-visual tutorials added
Redesigned GDR
Genera/Species Pages
Reference Transcriptome Analysis (RefTrans)
Reference Transcriptome Analysis (RefTrans)
Reference Transcriptome Analysis (RefTrans)
Reference Transcriptome Analysis (RefTrans)
Crop Ontology
Work in Progress
• Generating RefTrans for other Rosaceae species
• Implementing a comprehensive breeding
information management system (TripalBIMS)
Some Requests (Please)
• Cite us (Jung et al., 2014 – on website)
• Join our mailing list to receive biannual
newsletters and community communication
• Please tell us if you find a problem with the site,
have new functionality you would like
• Come to the GDR training workshop today 4 – 6
PM in the California room, GDR Demo Tues at
11.10 AM in the California room
• Come participate in the RosEXEC/RosIGI open
meeting Sunday 8-10,10-12 in the Hampton Room
Usage of GDR in 2016
o
o
o
o
19,821 visitors
58,710 visits
245,787 pages
149 countries
Funding and Acknowledgements