GNPAnnot Project 2010

Project 2010

Aims:

GNPAnnot is a project on green genomics which intends to develop a community system of structural and functional annotation supported by

comparative genomics and dedicated to plant and bio-aggressor genomes allowing both automatic predictions and manual curations of genomic objects. Gaëtan Droc1, Valentin Guignon1, Franc-Christophe

Baurens1, Vincent Jouffe1, Claire Poiron1, Juliette

Lengellé1, Olivier Garsmeur1, Mathieu

Rouard2_{,Stéphanie Bocs}1

2 CfL, Bioversity, Montpellier

Michael Alaux3, Leatitia Brigitte3, Delphine Steinbach Samson3, Erik Kimmel3, Cyril

Pommier3, Isabelle Luyten3, Nancy Terrier5, Philippe Leroy4, Hadi Quesneville3

4 UMR GDEC, INRA, Clermont 5 UMR SPO, INRA, Montpellier

Joelle Amselem6, Baptiste Brault6, Adeline

Simon6, Victoria Dominguez Del Angel6,

Claire Hoede6, Sabine Fillinger6, Michel

Meyer6_{, Thierry Rouxel}6_{, Marc-Henri}

Lebrun6

6 UMR BIOGER, INRA, Versailles 7 UMR BIO3P, INRA, Le Rheu

BIVI

8 UMR BIVI, INRA, Montpellier

References: http://www.gnpannot.org/ http://www.gmod.org Contact: stephanie.sidibe-bocs@cirad.fr michael.alaux@versailles.inra.fr fabrice.legeai@rennes.inra.fr joelle.amselem@versailles.inra.fr

Done with plant, insect, fungal genomic sequences:

- Predictions of protein-coding genes and transposable elements

- CAS core roundtrips: Chado, GBrowse, Apollo, Artemis - Feature, qualifier, value, annotation rule definitions

- Annotator training courses & manual curation of biological features - GMOD report development

- Chado controller development to manage access rights, annotation inspector & history

- In collaboration with GnpIntegr project, advanced search user interface / query builders: Biomart, Hibernate search (lucene)

- Communications (posters, talks, Web site) 1 UMR DAP, CIRAD, Montpellier

Fabrice Legeai7, Goulven Kerbellec9, Olivier Collin10,

Jean-Pierre Gauthier7, Emmanuelle d’Alençon8, François

Cousserans8, Philippe Fournier8, Denis Tagu7

9 _{Korilog SARL, Muzillac}

10 IRISA, INRIA, Rennes 3 URGI, INRA, Evry

Place Subject Unit Organism predicted curated current predicted curated current DAP Banana 7.13 1378 441 1298 3836 1279 2095 CfL Palm tree 0.27 43 30 41 5 5 9 Sugarcane 1.30 133 113 URGI Grapevine 480.00 26346 SPO GDEC Wheat 3B 18.21 175 175 10782 3222 3222 Botrytis 39.50 16360 1096 32 Leptosphaeria 44.90 12469 0 1850 472 Tuber 124.90 7496 1307 2520 0 BIO3P Aphid 460.00 34821 1926 34547 498474 ~800 498474 BIVI Lepidopteran 4.00 1086 70 1086 2027 0 2027 In progress Wheat & grapevine BIOGER Gene nb TE nb Genomic size (Mb) In progress Montpellier Versailles Rennes South & Tropical plants Fungi Insects

Component core Montpellier

Gene structure automatic annotation EuGène EuGène TriAnnot

Gene function & genome comparison in-house pipeline Funannot pipeline MAUVE

TE automatic annotation REPET REPET REPET

SGBD Postgres Chado Postgres Chado MySQL BioDBSeqFeat Postgres Chado

Genome browser GBrowse GBrowse GBrowse

Genome editor Artemis Apollo Apollo

Synteny Viewer _{Apollo Cmap}

Search & query builder _{Biomart Hibernate search Apache Lucene}

Versailles Rennes

Results:

Architecture of GNPAnnot CAS in three bioinformatics platforms

GNPAnnot CAS resource statistics

Database Storage CHADO

with controller

Gene Databanks

Uniprot (Swiss-Prot, TrEMBL) Genbank / EMBL / DDBJ

EST databanks

MSU (rice) / TAIR (arabidopsis)

TE Databanks

Repbase TREP

Plant Repeat Database Internal Ontologies Sequence Ontology Gene Ontology Feature Property Prediction pipeline Annotation storage Annotation Browser Annotation Editor GFF3 Query Builders Intermine BioMart

Hibernate search GnpIntegr

Comparative Genomics viewers

CMAP

GBrowse_syn

Apollo synteny viewer Artemis Comparison Tool

Genome Browsers

GBrowse with access rights GMOD report

Annotation history

Genome Editors

Apollo

Artemis with inspector

Gene automatic annotation

EuGene

Repeat automatic annotation

Structure Combiner (nucleotide)

- BLASTER / BLASTn - RepeatMasker - CENSOR - MATCHER - TRF - Mreps - BLASTER / tBLASTx

Other repeat analyses

- RepSeek - LTR_STRUC - LTR_Finder - LTRharvest - TE nest - FINDMITE REPET

Structure combiner (nucleotide)

- EugeneIMM - FGENESH - SpliceMachine - Gth - BLASTx Refinement

structure (nucleotide region) function (protein)

- Gth

- tBLASTn | prot4EST | frameDP

- Exonerate - BLASTp / BBMH - InterProScan Comparative Genomics - Ensembl Compara - Greenphyl

Other ISs (e.g. GnpIS)

DDBJ / EMBL / GenBank EST (GnpSeq, ESTtik)

Marker (SIReGal, TropGene) Metabolism (BioCyc, KEGG)

Interoperability faa GFF3 fna GFF3 EMBL fna faa db_xref EC_number

Team work (Wiki, Alfresco, JIRA, CVS/SVN, Drupal) GFF3 nwk clustalW Other storage Ensembl CMAP GBrowse_syn Intermine BioMart Flat files

Concept:

The Community Annotation System (CAS) is user-friendly, generic,

modular, portable, sustainable, upgradable and compatible

History

GBrowse

Artemis

GMOD report

Ongoing work:

- JBrowse

- Annotation extractors, reconcilers & updaters (new genomic sequence, new gene annotation, other gene annotation set, new assembly of a genomic sequence)

- Comparative genomics

- Bioinformatics platform exchanges

- Integration of annotation history in the GMOD report - Interoperability with other systems

- Communication (CECILL licences, publications)

Apollo