Citrusgreening.org: an Public Repository of Systems Biology Resources for the Huanglongbing (HLB) Disease Complex
Abstract: We have created an open access and public web portal with pathosystem-wide resources and bioinformatics tools for citrus, the vector Asian citrus psyllid (ACP) and multiple pathogens including Ca. Liberibacter asiaticus. This is the first example of a database to use the pathosystem as a more holistic framework to understand insect biology and disease transmission. The endeavor will connect and mine data sets generated by the community to study the citrus greening disease complex. We welcome submission of relevant data sets to enable sharing and allow the community to analyze data in an integrated system. The portal contains a variety of tools for omics data. DiaphorinaCyc and CitrusCyc pathway databases can be used to analyze transcriptomics and proteomics results to identify pathways with differentially regulated genes. Psyllid Expression Network (PEN) contains profiles of ACP genes from multiple life stages, conditions and hosts. Citrus Expression Network (CEN) contains public expression data for citrus from NCBI. All tools like JBrowse, Biocyc, Blast, CEN and PEN connect to a central database containing gene models for citrus, ACP and multiple Liberibacter pathogens. The portal also includes raw and annotated data from electrical penetration graph (EPG) recordings of ACP feeding on citrus and near relatives from published experiments. EPG datasets are extensive and only partially analyzed depending on particular questions of interest. Full datasets are released to encourage data mining and analysis by researchers interested in addressing questions related to ACP feeding behavior not addressed in our original publications. The portal includes user-friendly manual curation tools to allow the research community to continuously improve this knowledge base as more experimental research is published. Bulk downloads are available for all genome and annotation datasets from the FTP site (ftp://ftp.citrusgreening.org). The portal can be accessed at https://citrusgreening.org/. Non-technical summary: Citrusgreening.org is an open access and public web portal with information and omics resources for the host citrus, the vector psyllid and multiple pathogens including CLas. This data and resource hub is designed as a central repository for all data related to the citrusgreening disease complex. Scientists are encouraged to submit their data sets to the portal for sharing with the grower and research community.
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Citrusgreening.org: an Public Repository of Systems Biology Resources for the Huanglongbing (HLB) Disease Complex
- 1. www.citrusgreening.org Citrusgreening.org: an Public Repository of Systems Biology Resources for the Huanglongbing (HLB) Disease Complex Surya Saha Boyce Thompson Institute, Ithaca, NY ss2489@cornell.edu @SahaSurya IRCHLB, March 14th, 2019
- 2. www.citrusgreening.org Acknowledgements Mueller Lab Kansas State University Sue Brown USDA/ARS Michelle (Cilia) Heck (Cornell Univ./BTI) Wayne Hunter Robert Shatters Stephen L. Lapointe John S. Ramsey University of California, Davis Carolyn Slupsky Mirella Flores Prashant Hosmani Stephanie Hoyt University of Florida Lukasz Stelinski Justin George Cornell University Denis Willett Angela Kruse Indian River State College Tom D’elia
- 3. 500ng input DNA for Dovetail Chicago from single male psyllid Duplicated contigs added to alternate assembly Asian citrus psyllid(ACP) reference genome v1.1 v2.0 REFERENCE v3.0 REFERENCE Number of contigs 161,988 1,906 13 + unplaced Total bases 485 Mb 498 Mb 475 Mb Longest 1 Mb 4.2 Mb 50.3 Mb Contig N50 34.4 Kb 749 Kb 40Mb Ns 19.3 Mb 4.5 Mb 12Mb www.citrusgreening.org Chicago and Hi-C Poster: P9-101
- 5. Call for Data!! www.citrusgreening.org Resource Data types Psyllid Expression Network (PEN) RNAseq, proteomics and metabolomics data Citrus Expression Network (CEN) RNAseq, proteomics and metabolomics data Metabolic pathway database Lists of genes and pathways from publications. Curation of predicted pathways Manual gene curation Structural and functional annotation. Meta-data from publications for known or novel genes in citrus and the psyllid Data portal Electrical penetration graph, environmental, population genetics and other data sets Citrusgreening.org
- 6. Funding Available Sequencing • Illumina RNAseq • Pacbio long read RNAseq (Iso-seq) • Genomic sequencing • Single cell RNA sequencing Remote and On-site Training • Annotation • Web tools Bioinformatics Analysis • High performance computing • Genome assembly • Transcriptomics • Population genetics • Data analysis Database support • Web hosting • New web tools www.citrusgreening.org
- 7. www.citrusgreening.org AgriVectors Knowledge Base Data Producers Data Consumers Public Repository (remote) Pathosystem Repository (local and remote) Topic Repository (local and remote) Researchers Extension agents Industry USDA ARS / APHIS CRISPR / RNAi genes Microbiome Geospatial disease data Zebrachip Citrusgreening Pierce’s disease Researchers USDA ARS / APHIS / INRA IPM product development Outreach and extension Educators Secure portal Patents Commercial AgriVectors Portal NCBI / EMBL / DDBJ Ag Data Commons i5k
- 8. www.citrusgreening.org @Citrusgreening // @SahaSurya Thank you!! Posters: P10-175, P9-101, P10-120 Workshop (Thu, 6:30pm) Citrusgreening.org and Citrusgenomedb.org: What are they and how to use them? • Psyllid reference genome v3.0 • Manual curation of genes and pathways • Metabolic pathway databases • Psyllid Expression Network (PEN) • Citrus Expression Network (CEN)