Preliminary browser and BLAST interface released for v2 maize B73 reference genome

In March 2010 the Maize Genome Sequencing Consortium released the version 2 assembly of the maize B73 genome. This assembly effort, led by Fusheng Wei and Jianwei Zhang at the Arizona Genomics Institute with contributions from all Consortium members,is improved by the integration of

1. deep fosmid paired-end sequences from the WashU Genome Center
2. the maize optical map from Shiguo Zhou and David Schwartz at U. Wisconsin
3. sorghum-maize synteny analysis
4. additional Bac-based finishing by the Maize Gneome Sequence Consortium

For more information on the new assembly, designated B73 RefGen_v2, see the Arizona Genomics Institute maize project site. A revised annotation is in progress by Doreen Ware's team at Cold Spring Harbor and maizesequence.org and is expected in May.

The Phytozome team is happy to announce a preliminary genome browser for the v2 assembly, which allows users to BLAST against the masked and unmasked assembly, search by feature name, and view and download genomic regions in the context of

1. preliminary repeat annotations (courtesy of Shiran Pasternak at CSHL)
2. alignment of the predicted transcripts from the 4a.53 annotation from maizesequence.org
3. alignment of maize EST's and cDNA's, aseembled togehter on the genome using PASA
4. alignment of peptides from other grasses including sorghum, rice, and Brachypodium

Additional features coming soon include gene tracks (based on the upcaoming 5a.57 annotation from maizesequence.org) and Mo17 polymorphism data.

Note that since additional sequences have been captured in the new assembly, pseudomolecule coordinates from the v1 assembly used in the maize genome publications cannot be assumed to be unchanged. To locate your favorite locus in the new assembly, we suggest that you BLAST associated unique sequences (genomic or transcript) against the v2 assembly and zoom out as required to see the surrounding region.