CitrusCyc: Metabolic Pathway Databases for the C. clementina and C. sinensis Genomes

www.citrusgreening.org

CitrusCyc: Metabolic Pathway Databases for the C. clementina and C. sinensis

Genomes

Surya Saha1, Mirella Flores-Gonzalez1, Jodi L Humann2, Dorrie

Main2 and Lukas Mueller1

1Boyce Thompson Institute; 2Washington State University

[email protected] @SahaSurya

PAG XXV

Citrus Genome Workshop


Acknowledgements

Mueller Lab:

Mirella Flores

Prashant Hosmani

Main Lab:

Jodi Humann

Sook Jung


Citrus Genomics Resources

C. clementina genome

C. sinensis genome

C. trifoliata genome


Citrus Reference Genomes

• C. clementina (Clementine mandarin) v 1.0• 301.4 Mb with 1,398 scaffolds• 9 chromosomal pseudo-molecules (~21-51 Mb)• 24,533 proteins• 33,929 primary and alternate transcripts

• C. sinensis (Sweet orange) v 1.1• 319 Mb with 12,574 scaffolds• 236 scaffolds > 251 kb but no pseudomolecules• 25,376 proteins• 46,147 primary and alternate transcripts


Pathway Tools ConceptsPathway/Genome Database (PGDB) – combines information about

• Pathways, reactions, substrates

• Enzymes, transporters

• Genes, replicons

• Transcription factors/sites, promoters,

operons

Tier 1: Literature-Derived PGDBs• MetaCyc, HumanCyc, YeastCyc

• EcoCyc -- Escherichia coli K-12

• AraCyc – Arabidopsis thaliana

Tier 2: Computationally-derived DBs, Some Curation -- 34 PGDBs

• Bacillus subtilis, Mycobacterium tuberculosis

Tier 3: Computationally-derived DBs, No Curation -- The remainderSource: Peter Karp (SRI)


Pathway Tools ConceptsMetaCyc

2491 pathways from 2816 different organisms

Pathways involved in • Both primary and secondary metabolism• Associated metabolites, reactions, enzymes, and genes.

Enzyme Commission numbers (1.1.1.1)

• Numerical classification scheme for enzymes, based on the chemical reactions they catalyze.

• Recommended name

• Catalytic activity

• Cofactors (if any)

• Pointers to the Swiss-Prot protein sequence entrie(s) (if any)

7,000+ databases from many institutions world-wide. 5,000+ on BioCyc.org



Pathway/Genome Database Construction

Source: Peter Karp (SRI)

Genes Proteins Regulation Reactions Pathways

Enzyme Commission numbers from Uniprot


Pathway/Genome Database Construction

Annotated Genome

e.g. C sinensis

PathoLogic

Software

Reference Pathway

Database (MetaCyc)

Reactions

Pathways

Compounds

Gene

productsGenes

Pathway/Genome

Database (CitrusCyc)


Predicts metabolic pathways

Predicts which genes code for missing enzymes in metabolic pathways

Infers transport reactions from transporter names


Pathway Tools Software

Pathway/Genome

Editors

Pathway/Genome

Database

PathoLogic

Platform

Annotated

Genome

Pathway/Genome

Navigator

Briefings in Bioinformatics 11:40-79 2010

Genome-Scale

Flux Model



CitrusCyc


C sinensis Cyc v3.0http://pathways.citrusgenomedb.org/organism-summary?object=CSINENSIS_ML

• 25,376 proteins• 46,147 primary and alternate

transcripts• 38,964 transcripts have EC

numbers• 1217 unique EC numbers


C clementina Cyc v3.0http://pathways.citrusgenomedb.org/organism-summary?object=CCLEMENTINA_ML

• 25,376 proteins• 46,147 primary and alternate

transcripts• 28,630 transcripts have EC

numbers• 1179 unique EC numbers



Cellular Overview

Secondary metabolite biosynthesis Membrane pathways



Photosynthesis pathway











Overlay of RNAseq Results

Cellular Overview of Diaphorina citriBased on NCBI v100

Membrane proteins

Secretory proteins

Membrane proteins

Kruse et al. (unpublished)


Future Work

• Meta – CitrusCyc

• Manual curation of pathways


P0369

Dorrie Main


CitrusGreening.org

Host, Vector and Pathogen(s)

Blast Databases

BioCycs

JBrowse

FTP site

News

Publications

Social Media Twitter: 280 followersFacebook: 71 followers


P0368: Systems Biology Resources for the Citrusgreening Disease Complex

Mirella Flores


Thank you!!

Date post:	25-Jan-2017
Category:	Science
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CitrusCyc: Metabolic Pathway Databases for the C. clementina and C. sinensis Genomes

Science