MaizeGDB
jobs | upcoming events | sitemap
 | docs | bulk data | browse data | tools | login / register | links 
homeA popup window providing help for using the search form to the right  

CHECK HERE FOR UPDATES ON THE MAIZE SEQUENCING PROJECTS!

The NSF, USDA, and DOE announced their award of $32 million to the Washington University Genome Sequencing Center, Cold Spring Harbor, the Arizona Genome Institute, and Iowa State University on November 15, 2005. Information on the project can be accessed through the following links, and information about the B73 and Mo17 Chromosome 10 projects are posted here.


Project Updates

The maize B73 fosmid genomic library that was produced by Wash U to fill gaps and fill sequence in the BAC-based map, and importantly to be used as access to smaller clones for individual investigations, is now publicly available to the community. The end sequences of these fosmids have been deposited to GenBank Trace Archive and the clones are on MaizeSequence.org. The library was named Z_AI (by Wash U) and and individual clones as well as the full library are available from the AGI Resource Center for a nominal fee. A search engine to mate the GenBank Trace Archive number (to the Z_AI plate address of individual clones is available here. Note that the trace archive has a separate BLAST function from NCBI-BLAST which can be accessed here; notice the "pull down" on the database section- the maize fosmids are in "Zea mays - other" with other maize entries listed.

Use the feedback button at the bottom of any MaizeGDB page to report the correct the order of BACs within the physical map to the Maize Genome Sequencing Consortium!

2012 Status report for B73 RefGen_v3 (May 2012).
2007 Report written for the projects' advisory group (November 2007).

Status by subproject (PowerPoint).
2006 B73 (Wash U, CSHL, and AGI) | Mo17 (JGI) | Retro-Scaffolding (ISU)
2007 Overview | Maize Production Sequencing | Annotation and Visualization | BAC Assembly | Mo17 Shotgun Project and Outreach


Links

The Maize Genome Sequencing Consortium's genome browser: MaizeSequence.org
The Genome Sequencing Center's Maize Page for B73
B73 and Mo17 FISH image showing repetitive sequences (including knobs; courtesy of Jim Birchler)
Historical: Maize Genome Sequencing Information Portal (links to reviews of sequencing methods, the Request for Proposals, etc.)
AGI Maize Genome Contig Quality Table: AGI


Project Descriptions

B73 - A BAC by BAC approach
This effort - expected to require three years of work - will utilize a minimal tiling path of approximately 19,000 mapped BAC clones, and will focus on producing high-quality sequence coverage of all identifiable gene-containing regions of the maize genome. These regions will be ordered, oriented, and along with all of the intergenic sequences, anchored to the extant physical and genetic maps of the maize genome. Important features of the project include immediate release of preliminary and high-quality sequence assemblies, and the development of a genome browser that will facilitate user interaction with sequnece and map data.

Mo17 genespace by shotgun sequencing
A whole genome shotgun (WGS) strategy is expected to capture ~90% of the maize genome. The WGS strategy is to be assessed using Mo17 as a test case.


New! B73 Project Stock Information

The B73 source for the BAC libraries (BACs with prefix "b" prepared in Rod Wing's lab; BACs with prefix "c" prepared in Peter deJong's lab) was PI 550473. When requesting seed from the North Central Regional Plant Introduction Station, ask for any lot descended from the Coe PI 550473 lines.

The stock was received directly by the North Central Regional Plant Intoduction Station from Arnel Hallauer and has been maintained by the quality-maintenance procedures at the PI Station. Ed Coe reports that, "The results of QC lab checks for constancy in PI 550473 have been excellent."

The same source was used for the IBM mapping population. Maps produced at Missouri used 302 lines of this population, providing unmatched precision (resolution is at the intra-BAC level). These maps anchor the fingerprint-based contig assemblies to chromosome location.

High-Molecular-Weight DNA was prepared by Jack Gardiner in the lab at Missouri and shipped to Clemson (Wing's lab at the time) and to deJong's lab (just at the time his lab was moving to California) for BAC preparation.

NSF grant reports have documented the details, and specifics for the materials, preparation, characterization, and final assembly of the contig framework can be found in Coe E, Schaeffer ML (2005) Genetic, physical, maps, and database resources for maize. Maydica 50:285-303. Ed Coe has made a copy of that paper available here.


B73 Project Input Data Descriptions

The Physical Map
   Total Assembled Contigs: 721
         Equal to 2,150 Mb; 93.5% coverage of 2300 Mb genome
         Anchored: 421 ctgs; 86.1% the genome
         Average anchored contig size: 4.7 Mb
         Unanchored: 300 ctgs, 7.4% coverage
         Average unanchored contig size: 0.56 Mb
         189 of the 300 unanchored contigs are less than 10 clones
         Largest anchored contig 22.9Mb in Chr9
         Largest unanchored contig 6.7 Mb
   Total FPC Markers: 25,000
         STS markers: ~9,000
         Overgo Markers: 14,825
         Anchored markers: 1,918

The Tiling Path
   Using the physical map, ~3,200 seed BACs are being chosen with an average spacing of 800 kb. These seeds are required to have:
         1) at least one end sequenced,
         2) both agarose and HICF fingerprints,
         3) at least average insert size (~150 kb),
         4) at least one overgo match.
   Subsequently, BAC end sequences and fingerprint data are being used to extend the seed BACs into tiling path contigs for sequencing.


B73 Project Output Data Descriptions

Sequence traces:
   Automatically deposited to the Trace Archive at NCBI within 24 hours of production (includes fosmid ends).

BAC clone assemblies:
   Phase 1 HTGS_FULLTOP
         2 x 384 paired end attempts.
         Completed shotgun phase.
   Phase 1 HTGS_PREFIN
         Completed automated improvement phase.
         (Pending NCBI approval)
   Phase 1 HTGS_ACTIVEFIN
         Active work being done by a finisher.
   Phase 1 HTGS_IMPROVED
         Finished sequence in gene regions.
         Improved regions will be indicated.
         Once order and orientation of improved segments are confirmed, a comment will be added to indicate this.
         (Pending NCBI approval)

Example NCBI nucleotide search:
   Zea mays[ORGN] AND HTG[KYWD] AND Wilson[Author] - pulls the clone assemblies currently available.

Genome assemblies:
   Annotated BAC clones assembled in the context of mapping and other data, are to be displayed through a new Ensembl-based project site called The Maize Genome Browser (Doreen Ware, PI). This site will be dynamically updated as new data become available. There will be no built-in delays and new builds, annotation, and data will be made available as processing queues allow.


B73 Project Timeline

Year 1:
   Production sequencing for ~7,000 BAC clones (GSC).
   Sequence 0.55M (0.3X coverage) fosmid end pairs (GSC).
   Begin pre-finishing and finishing (GSC, AGI, CSHL).
   Finish ~4,500 BACs (GSC, AGI, CSHL)
   Begin genome assembly & annotation efforts (CSHL, ISU).

Year 2:
   Production sequencing for ~10,000 BAC clones (GSC).
   Finish ~10,000 BACs (GSC, AGI, CSHL).
   Continue genome assembly & annotation efforts (CSHL, ISU).

Year 3:
   Production sequencing for remaining BACs (GSC).
   Finish remaining (~4,500) BACs (GSC, AGI, CSHL).
   Continue genome assembly & annotation efforts (CSHL, ISU).


Return to the homepage

Last updated 1:49 pm, Dec 03, 2014.

home  

Be sure to cite us!

This page is HTML 4.01 valid!