Maize Genome Project

Maize Genome ProjectShiran PasternakJanuary 13, 2006

Gramene SAB MeetingSan Diego, CA

Shiran PasternakJanuary 13, 2006

Gramene SAB MeetingSan 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

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

Project Participants

Institutional Layout

Institutional Layout

•Annotation

•Visualization

CSHL FunctionsCSHL Functions

AnnotationAnnotation

•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 AnnotationInternal Annotation

•Iteratively redefine gene boundaries

•Provide new knowledge on maize genome

•Communicate status of the project

Public AnnotationPublic

Annotation

Annotation Pipeline

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?

VisualizationVisualization

ContigViewContigView

Synteny ViewSynteny View

* against Rice

GeneViewGeneView

New ViewsNew Views

InfrastructureInfrastructure

•Hardware

• 2 servers, forthcoming node cluster

•Dedicated architecture

• Genome browser

• Database schemata

• Annotation pipeline

Data ReleasesData Releases•Ongoing annotation updates (weekly)

• Repeats

• Gene models

•Infrequent genome builds (yearly?)

• Orthologs

• Syntenic Loci

Impact on Gramene

Impact on Gramene

•Cost: $0

•Maize browser will link to Gramene content

•Evolving requirements

StaffingStaffing

Principal InvestigatorsRick 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 TeamShiran Pasternak (Lead)

Apurva Narechania (Software)

Ben Faga (CMap)

Unnamed Data Analyst

Unnamed Software Developer

Thanks!Thanks!