South Green Bioinformatics activities at CIRAD
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1 South Green Bioinformatics activities at CIRAD Data Integration Team of the research unit DAP Manuel Ruiz, CIP, Lima, 23rd january
2 The Joint Research Unit DAP (Développement et Amélioration des Plantes = Plant Development and Genetic Improvement) : The 2 main research thematics focus on genetics and plant improvement & development and adaptation.
3 Studied species: rice, wheat, sorghum, sugarcane, banana, coconut, oil palm, yam, coffee, rubber tree, cocoa, cotton, apple and olive
4 Web portal information systems (IS) IS in development Haplophyle MS-DMind (very soon)
5 Information systems a database that manages genetic and genomic information about tropical crops banana, cocoa, coconut, coffee, cotton, oil palm, rice, rubber, sugarcane, sorghum an interactive information system for rice reverse genetics a database for the phenotypic characterization of the Génoplante rice insertion line library a Web portal for crossing cocoa phenotypic, genetic and genomic data rice rice cocoa
6 a database that manages genetic and genomic information about tropical crops Version 1.0 genetic map QTL data marker : RFLP, RAPD, SSR, etc. genotype data phenotype data germplasm data
7 a database that manages genetic and genomic information about tropical crops Chantal Hamelin Version 1.0 genetic map QTL data marker : RFLP, RAPD, SSR, etc. genotype data phenotype data germplasm data Xavier Argout,
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12 Gaétan Droc
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14 Pierre Larmande
15 Analysis A methodology for genome-wide searches for orthologs in plants Christophe Périn Matthieu Conte Mathieu Rouard (Bioversity) Analysis pipeline for cdna (secure access) Application for SSR marker development
16 Xavier Argout,
17 Xavier Argout, Jean-François Rami Claire Billot
18 Plants genomes sequencing species Genome size (Mb) Chromosomes number Arabidopsis thaliana Complete Oryza sativa Complete Populus trichocarpa Complete Vitis vinifera Complete Chlamydomonas reinhardtii Complete Sorghum bicolor Complete Medicago truncatula Complete Physcomitrella patens Complete Solanum lycopersicum In progress Triticum aestivum In progress Zea mays In progress C Périn
19 Analysis of plant genomes Species Clone Feature Musa acuminata Calcutta 4 Cavendish Grande Naine Pisang Musa balbisiana Klutuk Wulung wild banana Cultivated bananas are sterile, parthenocarpic, vegetatvely propagated plants wild banana Ploidy, Heterozygosity Heterozygous diploid AA Heterozygous triploid AAA Heterozygous diploid BB 40 BAC 6 BAC 18 BAC Musa acuminata Pahang doubled haploid Homozygous AA 2*600 Mb (2*11Χ) Roux & D'Hont Saccharum hybrid R570 Oryza sativa Japonica sugarcane Rice is a model organism for monocotyledon Heterozygous dodecaploid aneuploid (spontaneum and officinarum parents) diploid 12 BAC Data Organization Manager project Status Organism Family 2*430 Mb (2*12Χ) International Consortium for Sugarcane Biotechnology (ICSB) International Rice Genome Sequencing Project (IRGSP) D'Hont Droc Complete genome JGI Genoscope Submitted BAC Genoscope In progress complete genome complete Sorghum bicolor Sorghum diploid 2*800 Mb (2*10Χ) Rami genome JGI Elaeis guineensis Jacq African oil palm diploid 2*1000 Mb (2*16Χ) Billotte complete genome Arabidopsis thaliana Col-0 Thale cress is a model organism for dicotyledon diploid Theobroma cacao Criollo Cacao tree Homozygous diploid Global Musa Genomics consortium Rouard & Baurens 2*115 Mb (2*5Χ) International Collaboration international 2*380 Mb (2*10Χ) consortium of Lanaud cocoa genomics BAC NIAS complete genome complete genome In progress Done In progress To submit Done To submit Monocotyledon Dicotyledon Musaceae Poaceae Arecaceae Brassicaceae Malvaceae
20 Manual curation is not sufficient Function comment fields for all proteins in Swiss-Prot over time. Baumgartner bioinformatics 2007
21 project Develop a platform of structural and functional annotation supported by comparative genomics Dedicated to plant and bio-aggressor genomes Allowing both automatic predictions and manual curation of genes and transposable elements User-friendly, generic, modular, portable, sustainable, upgradable et compatible GDEC BIVI Spo
22 Instances
23 Instances Stéphanie Sidibe-Bocs Valentin Guignon Gaetan Droc
24 Information system model
25
26 Apollo Editors x
27
28 Find homologs using phylogenomic analysis GreenPhylDB use phylogenomic method to identify homologous genes I suggest that functional predictions can be greatly improved by focusing on how the genes became similar in sequence (i.e., evolution) rather than on the sequence similarity itself. Jonathan A. Eisen 1998
29 Homologs genes: orthologs and paralogs Orthologous genes are homologous genes that are descended from the last common ancestor through speciation and most probably encode proteins with a similar function in different species Speciation event Arabidopsis gene Rice gene A Orthologs Paralogs Gene duplication event Rice gene B Paralogous genes are referred as homologous genes that evolved through duplications and may encode proteins with more divergent functions
30 GreenPhylDB V1.0 Oryza sativa and Arabidopsis thaliana model plants Full genome available Gene annotation quality TAIR gene database release 8: gene ID like At1g12345 TIGR gene database release 5: gene ID like Os01g12345 Most of functional evidence.
31 Pipeline phylogénomique: GreenPhyl Low-complexity masking CAST FILTERING Splices selection Filtering procedure SS* LEON* Gene id indexing GI* Alignment MAFFT MULTIALIGNEMENT Alignment refinement Alignment masking Rascal AL2CO TREE CONSTRUCTION Bootstrapping alignement (x100) Genetic distance (x100) Tree construction (x100) SeqBoot ProtDist PHYML Rooting tree (x100) SDI ORTHOLOGS INFERENCE Set Bootstrap values on PHYML tree Gene id indexing Orthologs Inference SB* GI* DoRIO Output: Orthologs predictions (.txt & NHX files)
32 GreenPhyl phylogenomic pipeline Arabidopsis genes TAIR rice genes TIGR Automatic clustering procedure 6420 manually validated gene families 4400 phylogeneticaly analyzed gene families orthologs relationships between rice and Arabidopsis Probable same function
33 i-gost (Iterative GreenPhyl Orthog Search Tool) 2 objectives Get Add information on to a rice new or sequenced gene using information on to a rice new or sequenced arath with a gene using from information a new species available particularly from studied rice or arabidopsis? Gene with KNOWN? Query biological information Query Add biological information?? Gene with UNKNOWN function
34 GreenPhylDB V2.0 in progress Objectives 10 news fully sequenced genomes are now available (Populus alba, Glycine max, sorghum bicolor, Medicago truncatula, Vitis vinifera, Selaginella moellendorffii, Physcomitrella patens, Ostreococcus Tauri, Chlamydomonas reinhardtii, Cyanidioschyzon merolae ) Why do you integrate these species? 1. Complete sequencing and gene prediction 2. Will provide the complete list of plant gene families! 3. Use functional information available on these species 4. Reinforce phylogenomic signal and then orthologs predictions 5. Have a good taxonomy sampling
35 GreenPhylDB V2.0 A huge database ~390,000 sequences ~ 25,000 clusters 10 news species ~300,000 sequences GreenPhyl Database v2.0 2 species 81,000 genes 21,400 clusters 6,400 genes families GreenPhyl Database V1.0
36 Functional Annotation
37 Annotation fonctionnelle
38 Knowledge modeling of the structure-function relationships
39 The insulin receptor pathway
40 Knowledge modeling of the sequence-structure relationships
41 project
42 GCP Generation Challenge Programme A global consortium of crop research institutes established in 2003 with an approximately 10 year mandate to integrate comparative genomics and genetic resources molecular characterisation into plant breeding for stress tolerance, in particular, in drought-prone environments.
43 Generation Challenge Program GenDiversity is a query and analysis application combining genotyping data from diverse data sources, developed in support of diversity studies. Gautier Sarah Haplophyle, Methodology development for reconstruction of Genealogies based on Haplotypes related to geographic patterns (HaploPhyle: graphical haplotype network in the light of external data)
44 Data Integration
45 Data Integration non GCP DB Software analysis Platform Scientists GCP DB CIMMYT, CIRAD, IRRI, CIP, ICISAT, etc. Raw data
46 Platform architecture
47 Partnership SEG Agropolis Equipes biométrie Cirad X. Perrier L. Baudouin France SRG GS DIA-PC GDP INRA, Genoscope,CNG DGB GCP program Bioversity CIP, IRRI, CIMMYT, EMBRAPA, International ID DAR Swissprot GMOD consortium Biotec (Thailand) LIRMM O. Gascuel I. Mougenot CINES
48 Agropolis Plants Bioinformatics (genetics and genomics) UMRs DAP, DIAPC, BGPI, LSTM, SPO, RPB, BIVI, LGDP ATGC: LIRMM Bioinformatics platform Evolution Sequence analysis Analysis of gene expression Biological Ressources Genomics Genetic diversity Genetic Ressources New algorithms
49 High Power Computing CINES, Montpellier
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Supplementary Material Supplementary Table S1. Genomes available in build 47 Supplementary Table S2. Counts of putative contiguous gene split models in 39 plant reference genomes in build 47 Supplementary
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