An overview of the new species and improved gene function information present in PLAZA 3.0. URL: http://bioinformatics.psb.ugent.be/plaza/

1. PLAZA 3.0: an access point for plant
comparative genomics
Klaas Vandepoele
29 September 2014
VIB – Ghent University, Belgium

2. Overview
 Plant genomes: status & challenges
 Comparative genomics using PLAZA:
concepts & tools
 What’s new in PLAZA 3.0 ?
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3. Plant genome sequencing is booming
 New and faster sequencing
technologies
 Generating a draft genome sequence
has become cheap
 The number of published plant
genomes grows exponentially
 Unlocking biological information is
the real challenge
3 Michael & Jackson, 2013

4. Genome annotation
 Structural annotation shows
where genes are
 Describes their intron-exon gene
structure
 Functional annotation tells you
what genes do
 Can be downloaded along with the
genome sequence
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5. Comparative genomics
 Comparative genomics is a powerful
tool allowing us:
 to link genomic changes to
environmental adaptation
 to transfer knowledge from model
species to others plants
 to trace structural changes within a
genome trough time
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6. Comparative genomics has a steep learning curve
 A thorough knowledge of data
processing tools is required
 Computer clusters and high memory
machines are used
 New visualizations and methods are
necessary to explore genomic geatures
across multiple species
 Limited access to high-quality
comparative genomics information
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7. http://bioinformatics.psb.ugent.be/plaza/

8. http://bioinformatics.psb.ugent.be/plaza/

11. Gene families & genome organization
Gene family analysis
Genome analysis
>20 tools available!
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12. Exploiting cross-species genome information
 Centralized infrastructure
 Detailed gene catalog per species
 Structural annotation (gene models, UTRs)
 Functional annotation (experimental, sequence-based)
 Intuitive & advanced data mining tools for non-expert
users
• Sequence retrieval
• Gene functions
• Genome organization
• Pathway evolution
• Data manipulation
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Text-mining
Orthology-based

17. Comparative sequence analysis
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 Homology = shared ancestral common origin
 Inferred based on
 sequence similarity (BLAST)
 similar (multi-)domain composition & organization
TAIR
JGI
EMBL
BLASTCLUST
Tribe-MCL
Inparanoid
OrthoMCL
C/KOG
All-against-all sequence
similarity search (BLAST)

18. Gene families, Multiple sequence alignment &
Phylogenetic trees
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26K multi-gene families covering
90% of the total proteome
>1M proteins from
31 species
17K trees incl. 580K
annotated tree nodes

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20. Integrative Orthology Viewer
•Tree-based orthologs (TROG) inferred using tree reconciliation
•Orthologous gene families (ORTHO) inferred using OrthoMCL
•Anchor points refer to gene-based colinearity between species
•Best hit families (BHIF) inferred from Blast hits including inparalogs

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Gene colinearity & genome organization
Gene Homology Matrix (GHM)
i-ADHoRe 3.0
• Represent chromosomes as
sorted gene lists
• Identify all homologous gene
pairs between chromosomes (all-against-
all BLASTP).
• Score pairs of homologues in
matrix
1
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22. Genome-wide colinearity (WGDotplot)
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O. sativa
Z. mays

23. Multi-species colinearity
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24. PLAZA Workbench
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 Create a custom gene set (~experiment) using gene identifiers or
BLAST
 External/internal gene IDs (e.g. AN3, AT5G28640, GRMZM2G180246_T01)
 BLAST interface can be used to map sequence data from a non-model
species to a reference species present in PLAZA
 A toolbox is available to analyze user-defined gene sets
PLAZA
Workbench
WGMapping
Functional
annotations
Gene Families
GO enrichment
Tandem/block
duplicates
Sequence
retrieval
Microarray
transcript profiling
EST / RNA-sequencing
Genes reported
in Suppl. data
iOrthologs Export data…

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26. GO enrichment analysis
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27. What’s new in PLAZA 3.0?
 New genomes
 Dicots (13)
• Gossypium raimondii (cotton), Eucalyptus grandis
(eucalyptus), Solanum lycopersicum (tomato), Solanum
tuberosum (potato), Beta vulgaris (sugar beet), Prunus
persica (peach), Citrus sinensis (sweet orange), Cucumis
melo (melon), Citrullus lanatus (watermelon)
• Capsella rubella, Brassica rapa and Thelungiella parvula
• Amborella trichopoda
 Monocots (3)
• Musa acuminata (banana), Setaria italica (foxtail millet)
and Hordeum vulgare (barley)
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28. What’s new in PLAZA 3.0?
 Gene function information
 Free-text gene descriptions
• Primary data provider + UniProt
• AnnoMine* text-mining
 Protein domains
• InterPro
 Structured functional annotations
• Gene Ontology
• MapMan
• PlnTFDB and PlantTFDB
29 * Sofie Van Landeghem

29. Extended GO projection
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Orthology-based
Homology-based
Transfer of experimentally confirmed GO information to orthologs and homologs

30. Coverage gene function information
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Gene Ontology (Biological Process)
Gene descriptions
blue = primary GO; green = GO projection (orthology + homology)

31. Conclusions
 PLAZA 3.0 provides a versatile toolbox for plant genomics
 Integration of complementary data sources describing gene
functions
 Improved algorithms to transfer functional annotation from
well-characterized plant genomes to other species
 Technical improvements
 database design
 comparative genomics tools
 speed
 visualizations
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Acknowledgments
• – plant comparative genomics
 Sebastian Proost
 Michiel Van Bel
 Dries Vaneechoutte
 Yves Van de Peer
 Dirk Inzé
plaza_genomics
http://bioinformatics.psb.ugent.be/plaza/