Work completed

2023

  • [Data] 4 new expression datasets added to heatmap tool (9/20/2023)
  • [Data] C. sinensis cv. Newhall genome v1.0 added to CGD, JBrowse, BLAST, Synteny Viewer (9/1/2023)
  • [Outreach] Monthly CGD email with a video trait to GWAS to gene to ortholog (8/29/2023)
  • [Data] Added differentially methylated region data from 1 paper in C. sinensis JBrowse (8/23/2023)
  • [Data] Added C. maxima Cupi Majiyou v1 and F. hindsii S3y-45 v2 CitrusCycs (8/10/2023)
  • [Data] Added 1 genetic map and 2587 SNP markers from Kumar et al 2023 (8/8/2023)
  • [Outreach] July 16, 2023 - BIMS and FieldBook at the Breeding Tools Workshop, National Association of Plant Breeding Annual Meeting (7/26/2023)
  • [Outreach] July 2023 CGD Newsletter sent (7/24/2023)
  • [Outreach] Monthly CGD email with a video on how to search and view traits and associated data (6/29/2023)
  • [Outreach] Monthly CGD email with a video on how to search and view GWAS data (5/30/2023)
  • [Data] Added 19 QTL, 1 map, 18 markers from Zheng et al, 2018. (5/22/2023)
  • [Data] Added data from Matsumoto et al, 2022 (7 QTL, 1 map, 119 markers) and Yang et al, 2022 (5 QTL, 1 marker) (5/17/2023)
  • [Tools] Genotype Search enabled on CGD (5/11/2023)
  • [Data] F. hindsii v2.0 and C. maxima Cupi Majiayou genomes added (5/11/2023)
  • [Data] C. limon Eureka and C. australis added to CitrusCyc (5/11/2023)
  • [Data] Seven new Citrus genomes added to Synteny Viewer (5/10/2023)
  • [Data] Added data from Montalt et al, 2023 (2071 SNPs, 2 genetic maps, 93 GWAS and gene associations and genotyping for 2 SNPS) (5/9/2023)
  • [Data] GWAS data (52 GWAS, 41 genetic marker, 41 gene associations, 23 traits) added from Mattia et al. 2022 (5/9/2023)
  • [Tools] QTL/GWAS search added to CGD (5/9/2023)
  • [Data] 5 additions to CitrusCyc: C. sinensis Valencia v2.0 (HZAU), C. sinensis Valencia DVS_A and DVS_B, C. sinensis DHSO. P. trifoliata ZK8 (5/4/2023)
  • [Data] Citrus limon cv. Eureka and Citrus australis (UQ) genomes added (5/3/2023)
  • [Outreach] April 2023 CGD Newsletter sent (4/26/2023)
  • [Data] 4 new C. sinensis and 1 new P. trifoliata genomes added to chado, JBrowse, BLAST (4/19/2023)
  • [Outreach] Monthly CGD email with Genetic Map and Genome Correspondences video (3/30/2023)
  • [Tools] BIMS imports images from Field Book (3/2023)
  • [Tools] Ortholog page added to gene/mRNA page (3/2023)
  • [Outreach] Monthly CGD email with New Marker Search video (2/23/2023)
  • [Tools] BIMS now supports BrAPI v1 and v2 Field Book calls (2/2023)
  • [Tools] Toolbar for selecting colors for GWAS display in MapViewer (2/2023)
  • [Tools] MegaSearch updated to allow searching records with empty fields (e.g. for searching genes without any functional annotation) (2/2023)
  • [Tools] Crosslink between CGD and Fruit and Nut Database (2/2023)
  • [Outreach] January 2023 CGD Newsletter sent (1/31/2023)
  • [Tools] Gene annotation template and loader created (1/2023)
  • [Tools] MegaSearch updated to query GWAS (1/2023)
  • [Tools] MapViewer updated to display GWAS data (1/2023)
  • [Outreach] PAG NRSP10 Workshop on database usage and tools (1/15/2023)

2022

  • [Outreach] Monthly CGD email sent (12/22/2022)
  • [Tools]Template/loader for GWAS data created (12/2022)
  • [Outreach] Monthly CGD email with Overlay Omics Data in CitrusCyc video (11/28/2022)
  • [Tools] BIMS/MCL made compatible with PHP8 (11/2022)
  • [Outreach] October 2022 CGD newsletter sent (10/31/2022)
  • [Tools] MegaSearch Ortholog/paralog search added (10/28/2022)
  • [Tools] TripalMap v2.0 released (10/2022)
  • [Tools] ChadoSearch v2.7 for Drupal 7 released (10/2022)
  • [Tools] Tripal MegaSearch v1.4 for Drupal 7 released (10/2022)
  • [Outreach] Monthly CGD email with BLAST to mRNA details to JBrowse video (9/27/2022)
  • [Outreach] Monthly CGD email with MegaSearch for Genetic Maps video (8/30/2022)
  • [Tools] Data templates - ORCID/DOI enabled in data loading templates (8/2022)
  • [Tools] BIMS - Trait descriptor export (BIMS-Field Book) through BrAPI enabled (8/2022)
  • [Tools] MegaSearch - Accordion style form added in query section (8/2022)
  • [Tools] MapViewer - Resolution of the map comparison view improved (8/2022)
  • [Tools] New search pages available for Trait and Trait Descriptor (8/2022)
  • [Tools] Trait and dataset pages updated with more hyperlinks (8/2022)
  • [Outreach] CGD presentation at 2022 ASHS Conference (8/1/2022)
  • [Outreach] July 2022 CGD Newsletter sent (7/26/2022)
  • [Tools] Mapviewer - layout of the landing page improved (7/2022)
  • [Data] C. limon assemblies added to Synteny Viewer (July 2022)
  • [Outreach] Monthly CGD email with MegaSearch for QTL video (6/27/2022)
  • [Tools] New corresponding matrices in MapViewer (6/2022)
  • [Tools] MapViewer and map page updated to display details of bin map (6/2022)
  • [Tools] Created ‘bin’ pages with Map/LG/marker/QTL information (6/2022)
  • [Outreach] Monthly CGD email with BLAST tool video (5/31/2022)
  • [Outreach] April 2022 CGD Newsletter sent (4/28/2022)
  • [Tools] Ortholog/paralog search added (4/5/2022)
  • [Outreach] Monthly CGD email with Marker Search video (3/24/2022)
  • [Outreach] Monthly CGD email with MapViewer video (2/24/2022)
  • [Outreach] 2nd CGD Newsletter released (1/28/2022)

2021

  • [Outreach] 2021 CGD year-end review sent to mailing list (12/14/2021)
  • [Data] Lemon haplotype assemblies (primary and alternative) added to chado, JBrowse, BLAST, and CitrusCyc (12/20/2021)
  • [Outreach] Added Newsletter page and sent first CGD Newsletter (9/27/2021)
  • [Data] New Citrus spp. data: maps (2), markers (4158) (6/16/2021)
  • [Data] Updated Citrus NCBI gene and mRNA data, added 6261 new sequences (5/28/2021)
  • [Data] F. hindsii and P. trifoliata added to SyntenyViewer (4/2/2021)
  • [Data] Protein sequences for Ca. LIberibacter genome uploaded to Chado (3/9/2021)
  • [Data] Protein sequences for all Citrus (and related genera) genomes uploaded into Chado (3/5/2021)
  • [Data] F. hindsii PathwayCyc added (2/24/2021)
  • [Data] Fortunella hindsii v1 genome added to Chado database, Blast, JBrowse (1/29/2021)
  • [Data] New Citrus spp. data: markers (53), maps (1), traits (2), QTL (11) (1/4/2021)

2020

  • [Data] New Citrus spp. data: markers (1036), maps (2), traits (2), QTL (13) (12/11/2020)
  • [Data] New Citrus sinensis data: markers (49) (12/11/2020)
  • [Data] New Citrus grandis data: markers (268) (12/4/2020)
  • [Data] New Citrus clementina data: markers (4) (12/4/2020)
  • [Data] New Citrus spp. data: markers (189), maps (1) (12/4/2020)
  • [Data] P. trifoliata (JGI) PathwayCyc added (12/2/2020)
  • [Data] Poncirus trifoliata (JGI) genome added to CGD, JBrowse, BLAST (11/12/2020)
  • [Data] New Citrus spp. data: markers (1252), maps (5), QTL (52) (7/16/2020)

2019

  • [Data] Four new CitrusCycs added.  These were generated by GCD. C. medica, C. maxima, C. ichangensis, A. buxifolia (12/19/19)
  • [Data] Added 115 SNP markers for C. clementina (10/29/19)
  • [Tools] JBrowse updated to v1.16.4 (6/4/19)
  • [Tools] MegaSearch and Trait and Descriptor Searches added (5/31/19)
  • [Data] New map added: Citrus-Murcott_x_Pera-F1 (5/22/2019)
  • [Data] New data added: mRNA (42,676), germplasm (47), maps (2), markers (1,488), publications (289), QTL (18), agronomic traits (2) (07/2018 - 04/2019)
  • [Tools] Enabled Omics Dashboard and SmartTables for Pathway Tools (March 2019)
  • [Data] Added InterProScan and BlastX analysis data for bacterial CDS sequences.  Added CDS option to sequence type under Sequence Search interface for bacterial CDS sequences (March 2019)

2018

  • [Data] Bacteria genome synteny analysis added to Synteny Viewer (October 2018)
  • [Data] Citrus reticulata v1.0 (HZAU) loaded into chado, JBrowse, BLAST.  Homology analyses with sprot and TrEMBL also done and excel file available for download.  InterProScan and blastx results also loaded into chado. (September 2018)
  • [Data] CLas JXGC genome loaded into chado, JBrowse, and BLAST (September 2018)
  • [Tools] MapViewer updated to Tripal 3 version.  Now can export figures of maps, correspondence matrices, and dot plots. (August 2018)
  • [Tools] CGD converted to Tripal v3 and Elastic Search and Cross-Site search enabled (August 2018)
  • [Data] Best-hit protein homology results from TrEMBL available to download for C. sinensis v2.0, C. medica, C. maxima, and A. buxifolia genomes (July 2018)
  • [Tools] Genome synteny analysis for Citrus genomes and New Synteny Viewer module added (June 2018)
  • [Data] Best-hit protein homology results from SwissProt available to download for C. sinensis v2.0, C. medica, C. maxima, and A. buxifolia genomes (June 2018)
  • [Data] About 913 more Citrus sp. NCBI genes were imported into the database (June 2018)
  • [Data] As of June 22,2018—GCD contains: 70 genetic maps, 48,145 markers, 579 QTLs
  • [Tools] MapViewer updated with dynamic drawing element positioning for QTLs and Correspondences (June 2018)
  • [Tools] Breeding Information Management System (BIMS) added to CGD, USDA-GRIN phenotype data added to BIMS for public access (June 2018)
  • [Data] InterProScan analysis of all Citrus genomes loaded into Chado, BLAST analysis with SwissProt database also loaded into Chado (June 2018)
  • [Data] Genome assemblies of Citrus maxima (C. grandis), Citrus ichangensis (C. cavaleriei), Citrus medica, and Atalantia buxifolia were added to CGD database, JBrowse and BLAST (April 2018)

2017

  • [Data] Since April 2017, 13 more maps, 12108 markers, and 138 QTLs have been added (December 2017)
  • [Website Improvement] CGD User's Manual added (September 2017)
  • [Data] Valencia orange genome added to CGD (July 2017)
  • [Data] Updated and added NCBI SRA Datasets (May 2017)
  • [Data] Added 50 maps to CMap (May 2017)
  • [Data] Added 50 maps, 30,130 markers, and 341 QTLs to the database (April 2017)
  • [Data] Added SRA data from 30 citrus genomes aligned to the C. clementina v1.0 genome (March 2017)
  • [Data] Added Liberibacter genomes to database, BLAST, and JBrowse (March 2017)
  • [Website Improvement] Updated website to new interface style (March 2017)
  • [Tools] MapViewer map visualization tool added (March 2017) 
  • [Tools] Implemented new Tripal BLAST module with linkouts to JBrowse and the database (March 2017)
  • [Tools] Moved all Citrus genomes from GBrowse to JBrowse (March 2017)
  • [Data] Added C. sinensis v1.1 to database, BLAST, and JBrowse (March 2017)
  • [Data] Updated NCBI genes (1/4/17)