1. Resources for HLB and Citrus Genomics, Genetics and Breeding Research
Jodi Humann, Morgan Frank, Sook Jung, Chun-Huai Cheng, Taein Lee, Heidi Hough, Katheryn Buble, James Crabb, Ping Zheng, Kristin Scott, Julia Piaskowski, Mirella Flores, Surya Saha, Lukas A. Mueller, Fred Gmitter, Albert Abbott, Dorrie Main

2. Why CGD?
Single website to view, search, and download citrus related genomics, genetics and breeding data
Easy-to-use interfaces
Multiple tools available
Can be tailored to suit the needs of the research community
Uses an open-source database platform with many groups worldwide developing new modules

3. Funding National Research Support Project USDA-NIFA PI D. Main – WSU
5 yr. renewal submitted ($2.5 M)
Plant Genome Research Program
PI D. Main – WSU
$2.99 M
Through June 2020

4. CGD Steering Committee
Formalized steering committee convened at 2019 Plant and Animal Genome Conference
Fred Gmitter
UF-CREC
Mikeal Roose
UC Riverside
Danelle Seymour
Manuel Talon
IVIA
Marco Takita
IAC-Brazil

6. Species Overview Page

7. Species Overview Page

8. Genomic Resources Citrus genomes
C. clementina cv. Clemenules, v0.9 and v1.0, JGI
Aligned SRA data to v1.0 from Wu et al and M. Roose also available in JBrowse
C. sinensis cv. Ridge Pineapple, v1.0 and v1.1, JGI
C. sinensis cv. Valencia, v2.0, HZAU
C. maxima (C. grandis), v1.0, HZAU
C. ichangensis (C. cavaleriei) cv. XJC, v1.0, HZAU
C. medica cv. X2, v1.0, HZAU
C. reticulata cv. WM01, v1.0, HZAU
Atalantia buxifolia cv. HKC, v1.0, HZAU
Liberibacter genomes
Complete NCBI genomes
CLas (5)
CLam (1)
CLaf (1)
CLso (1)
L. crescens (2)

9. Genomic Resources - Tools
Available for all genomes
Gene and Transcript search
Sequence search
JBrowse
BLAST+
Synteny Viewer (All Liberibacter and 4 citrus genomes)
Also have PathwayCyc for C. clementina and C. sinensis genomes
Provided by Lukas Mueller’s Lab, Boyce Thompson Institute, Cornell

10. Gene and Transcript Search

11. Gene and Transcript Search

12. Sequence Search

13. Sequence Search

14. Gene and mRNA Feature Pages

15. Gene and mRNA Feature Pages

16. JBrowse

17. BLAST+

18. BLAST+

19. BLAST+

20. BLAST+

21. Synteny Viewer
Module provided by Fei Bioinformatics Lab, Boyce Thompson Institute

22. Synteny Viewer

23. Synteny Viewer

24. Synteny Viewer

25. Synteny Viewer

26. Synteny Viewer

27. Genetic Resources
Searchable markers, genetic maps, QTLs from published literature
MapViewer tool to view and compare genetic maps
Data Type
Total Number
Markers
48,241
Genetic Maps 70
QTLs
579 (212 traits)
Germplasm
1,426
Phenotypic measurements
23,070 (38 trait descriptors)

28. Marker Search

29. Marker Search

30. QTL Search

31. QTL Search

32. MapViewer

33. MapViewer Draggable section adjusts close-up view of linkage group
Marker and QTL info displayed when cursor hovers over name
Clicking on marker and QTL name opens a feature page with more details

34. MapViewer – Control Panel

35. MapViewer – Comparing Maps

36. MapViewer – Dot Plot

37. PathwayCyc

38. Breeding Information Management System (BIMS)
Online breeding management system
Store, manage, archive and analyze private breeding program
Load data with provided templates
Import data from Field Book (Android App)
Publicly available breeding data
USDA-GRIN phenotype data

39. Breeding Information Management System (BIMS)
Future BIMS development
Users will be able to integrate private data with publicly available genomic, genetic and breeding data in the community database
Utilize user-provided pedigree, phenotype and genotype data in performing genomic analysis and making breeding decisions.
Use open-source new genomics tool and breeding decision tools with seamless access to HPC

40. BIMS

41. CGD Future Development
Addition of transcript expression data from citrus
Pedigree data viewer for modern pedigree data
Add more citrus resequencing data to JBrowse and for download
Phenotype data from citrus rootstock
Correlate gene names between JGI and HZAU C. sinensis genomes
Citrus species naming/synonym information
Curate pathogen/host gene interactions
GenSAS Community

42. GenSAS – Genome Sequence Annotation Server
Completely web-based
Free user accounts
Easy-to-use interfaces
Detailed User’s Guide

43. Eukaryote annotation workflow
Upload Sequences
PRINSEQ-lite, BUSCO
Create Project
Upload Evidence
Identify Repeats
RepeatMasker, RepeatModeler
Mask Sequences
Align Evidence
BLAST, BLAT, DIAMOND, HISAT2, PASA, TopHat
Structural Annotation
Augustus, BRAKER2, GeneMarkES, Genscan, GlimmerM, SNAP, RNammer, tRNAScan-SE
Choose Official Gene Set
EvidenceModeler (optional)
Refine Gene Models
PASA (optional)
Functional Annotation
BLAST, DIAMOND, InterProScan, Pfam, SignalP, TargetP
Manual Curation
Apollo, JBrowse
Generate Files for Publication
BUSCO

44. Once jobs are in queue, users can log out of GenSAS
GenSAS Interface
Once jobs are in queue, users can log out of GenSAS

45. Annotate Step – Manual Curation
Edits added to “User-created Annotations” will be merged into final results

46. GenSAS Community
A new Tripal extension for community databases using Tripal
Tool for managing multi-user, manual curation of genomes
Results from GenSAS Annotation Project
GFF3 files from other annotation tools
GenSAS Community
Improved genome annotation

47. GenSAS Community Roles
Lead Curator:
Manage project
Review and approve curations
Assistant Curator:
Perform manual curations
Submit for review
Guest Curator:
View-only access

48. GenSAS Community Roles
Genome region assigned
Lead
Curator(s)
Assistant
Curator(s)
Approve annotations
Submitted for approval
Community Database
Manual curation
GenSAS Community Genome Project
Improved annotations added to database

49. Acknowledgements Sign up for the CGD Mailing list from the website
Citrus Research Community
To learn more about CGD:
Poster IRCHLB-P10-176
Sign up for the CGD Mailing list from the website