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2017 ASHS Annual Conference

Citrus Genome Database: Resources That Enable Basic, Translational, and Applied Research

Thursday, September 21, 2017: 11:00 AM
Kohala 1 (Hilton Waikoloa Village)
Doreen Main, Washington State University, Pullman, WA
Jodi L. Humann, Research Assoc., Washington State University, Pullman, WA
Morgan Frank, Washington State University, Pullman, WA
Julia Piaskowski, Dr, Washington State University, Pullman, WA
Sook Jung, Washington State University, Pullman, WA
Chun-Huai Cheng, Washington State University, Pullman, WA
Taein Lee, Washington State University, Pullman, WA
Kristin Scott, Washington State University, Pullman, WA
Ping Zheng, Washington State University, Pullman, WA
Mirella Flores, Boyce Thompson Institute, Ithaca, NY
Surya Saha, Boyce Thompson Institute, Ithaca, NY
Lukas Mueller, Boyce Thompson Institute for Plant Research, Ithaca, NY
Fred Gmitter, University of Florida, Lake Alfred, FL
Albert Abbott, University of Kentucky, Lexington, KY
The Citrus Genome Database (CGD, www.citrusgenomedb.org) is being developed as a one-stop resource for citrus genetics, genomics, and breeding research. In this presentation we highlight CGD features that provide the citrus community with data and tools to combat Huanglongbing (HLB). The database has been redesigned and features a streamlined user interface that allows for quick access to data and tools and is also mobile friendly. It contains curated citrus genetic marker, map, and QTL data, genome data for clementine and sweet orange, as well as annotated reference transcriptomes (RefTrans) generated by analysis of published RNA-Seq and EST datasets. The database also has the most up-to-date version of CitrusCyc v3.0 which includes metabolic maps for the C. clementina and C. sinensis genomes. Tools such as BLAST for searches against the genome sequences, JBrowse for viewing genomes, and CMap/MapViewer for viewing and comparing genetic map data are also available on CGD. In addition to the tools to view and search published data in CGD, the Breeding Information Management System (BIMS) allows breeders to upload their data via the web, or directly from the Field Book app, to a private account. The private data than can be analyzed in conjunction with the public data. In addition to citrus data, the genomes of the different ‘Candidatus Liberibacter’ species and psyllid vector are available in CGD in JBrowse and the sequence data is searchable with the BLAST tool. As a community resource, CGD is being developed based on user feedback with the goal of providing the data and tools that will enable citrus crop improvement. CGD is supported by USDA-NRSP10, NSF-PGRP, and USDA-SCRI.
See more of: Citrus Crops 2 (Oral)
See more of: Oral Abstracts