Maize Genome Project Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego, CA Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego,

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Maize Genome Project Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego, CA Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego, CA

3 year sequencing effort Funded November, 2005 Objectives Sequence the maize genespace Genic and regulatory regions Finish 721 contigs: 1 in 100,000 error rate Anchor to physical and genetic maps Maize Genome Project

Arizona Genome Institute (AGI) Mapping Washington University at St. Louis (WU) Sequencing Cold Spring Harbor Laboratory (CSHL) Analysis and Annotation Project Participants

Institutional Layout

Annotation Visualization CSHL Functions

Annotation Internal Public

Prefinishing: Automated Enrich BAC assemblies with AutoFinish ‘Do Not Finish’ repeat tags Finishing: Manual Tag mRNA and ESTs to target problematic regions Internal Annotation

Iteratively redefine gene boundaries Provide new knowledge on maize genome Communicate status of the project Public Annotation

Annotation Pipeline Gramene-Ensembl Whole genome alignment to rice ab initio gene prediction with Fgenesh Evidence-based gene prediction Repeat analysis Full annotation on nearly finished BACs

Gramene and Ensembl Browser Existing: Contigs, Genes, Synteny CMap Views Whole genome alignment Sequencing status of BACs & Contigs Other track suggestions? Visualization

ContigView

Synteny View * against Rice

GeneView

New Views

Infrastructure Hardware 2 servers, forthcoming node cluster Dedicated architecture Genome browser Database schemata Annotation pipeline

Data Releases Ongoing annotation updates (weekly) Repeats Gene models Infrequent genome builds (yearly?) Orthologs Syntenic Loci

Release Timeline March, 2006 Annotation Pipeline Launch of Weekly Updates July, 2006 January, 2007

Impact on Gramene Cost: $0 Maize browser will link to Gramene content Evolving requirements

Staffing Principal Investigators Rick Wilson (WU) Sandra Clifton (WU) Pat Schnable (IA) Srinivas Aluru (IA) Rod Wing (AGI) Rob Martienssen (CSHL) Dick McCombie (CSHL) Doreen Ware (CSHL) Lincoln Stein (CSHL) CSHL Team Shiran Pasternak (Lead) Apurva Narechania (Software) Ben Faga (CMap) Unnamed Data Analyst Unnamed Software Developer

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