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 jhumann@wsu.edu, dorrie@wsu.edu www.citrusgenomedb.org

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

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

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

Species Overview Page

Species Overview Page

Genomic Resources Citrus genomes C. clementina cv. Clemenules, v0.9 and v1.0, JGI Aligned SRA data to v1.0 from Wu et al. 2014 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)

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

Gene and Transcript Search

Gene and Transcript Search

Sequence Search

Sequence Search

Gene and mRNA Feature Pages

Gene and mRNA Feature Pages

JBrowse

BLAST+

BLAST+

BLAST+

BLAST+

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

Synteny Viewer

Synteny Viewer

Synteny Viewer

Synteny Viewer

Synteny Viewer

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)

Marker Search

Marker Search

QTL Search

QTL Search

MapViewer

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

MapViewer – Control Panel

MapViewer – Comparing Maps

MapViewer – Dot Plot

PathwayCyc

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

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

BIMS

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

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

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

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

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

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

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

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

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 www.citrusgenomedb.org