Maize Production Sequencing

Maize Production Goals BAC End Sequencing of 220,000 Clones Fosmid End Sequencing of 500,000 Clones Shotgun of 16,000 BAC Clones

Maize BAC End Sequences 580,000 reads processed 567 average read length 60% success

Maize Fosmid End Sequences 850,000 processed 79% success 543 average read length Completed today

Library Construction Pipeline Receipt of sheared DNA from AGI Size selection of insert DNA Ligation into pSMART vector

Constructed 17,034 Libraries as of August 31st

Average Fail Rate for Library Construction was less than 5%

3.5X coverage Clone size verification 50% paired ends BES agreement 25% of clones failed 22% need more data 3% BES disagreement Shotgun Criteria

Shotgun Complete for 12,211 Clones as of August 31st

Final Production Work 660 Clones Need Library Construction 2100 Clones In Production Pipeline Expected Completion Date December 2007

Sequence Improvement Bob Fulton Dick McCombie Rod Wing

Sequence Improvement Pipeline Shotgun_done triggers the prefinishing pipeline Initial identification of do finish regions Manual sorting and use of autoedit(Gordon) to break apart misassembly. Autofinish(Gordon) used to choose directed reactions for all gaps and regions of low quality in do finish regions Reassembly and 2nd iteration of prefinishing pipeline Final identification of do finish regions and handoff to finishing pipeline

Clone Improvement through the Prefinishing Pipeline

End Spanning Plasmids Coverage (green) Assembly View-Entire Clone

Repeat Tags Do Finish GSS sequence EST sequence Assembly View-Do Finish Region

Alignment with cDNA read pairs Alignment with End Sequences

ActualProjected

Maize GenBank Submissions Joanne Nelson

Submission Landmarks HTGS_FULLTOP HTGS_PREFIN HTGS_ACTIVEFIN HTGS_IMPROVED

Improved Sequence Non-repetitve portions of the sequence have had sequence improvement (directed attempts) and have been labeled as improved. Improved regions are double stranded, sequenced with an alternate chemistry or covered by high quality data (i.e. phred quality greater than or equal to 30 or approval by an experienced finisher), unless otherwise noted. Regions of low sequence complexity (such as dinucleotide repeats and small unit tandem repeats) in the improved regions have not been resolved to previously established finishing standards. BAC end sequence, cot and methyl filtered genome survey sequence and data from overlapping projects of strain B73 may have been included in this project. Where possible, contigs have been ordered and oriented based on read pairing. These regions are designated as scaffolds. Additional order and orientation will be provided upon completion of detailed analysis of the complete finished tiling path.

Improved Sequence FEATURES Location/Qualifiers source /organism="Zea mays" /mol_type="genomic DNA" /db_xref="taxon:4577" /chromosome="1" /clone="CH J17; ZMMBBc0132J17" misc_feature /note="scaffold_name:Scaffold1" misc_feature /note="assembly_name:Contig28 vector_side:SP6" misc_feature /note="Improved sequence." unsure /note="Non-repetitive but unresolved region" gap /estimated_length=unknown misc_feature /note="assembly_name:Contig27" misc_feature /note="Improved sequence." unsure /note="Non-repetitive but unresolved region" misc_feature /note="Improved sequence." gap /estimated_length=unknown misc_feature /note="assembly_name:Contig14" gap /estimated_length=unknown misc_feature /note="scaffold_name:Scaffold2

Submission Totals HTGS_FULLTOP3342 HTGS_PREFIN2014 HTGS_ACTIVEFIN4151 HTGS_IMPROVED2660 TOTAL 12167