The B73 Maize Genome Sequence: B73 RefGen_v2

March 31, 2010

The NSF funded Maize Genome Sequencing Consortium is pleased to announce the release of a significantly improved version of the B73 Maize Genome Sequence: B73 RefGen_v2.

Since the first release of the B73 RefGen_v1 on March 20, 2009, we have made a number of additional improvements to the maize genome sequence, especially with respect to ordering and orienting sequence contigs within BACs. These Improvements include: a) incorporation the new or update of BAC/fosmid clones (~2,000), b) ordering and orienting sequence contigs within BACs using paired-end fosmid sequence data, c) ordering and orienting sequence contigs within BACs and across contigs using sorghum-maize synteny, and d) ordering and orienting physical contigs based on the maize optical map. The resultant B73 RefGen_v2 genome sequence is composed of 417 physical contigs that are anchored to the maize genetic map (vs. 405 in v1; 99.2% of the genome), and 19 unanchored contigs (vs. 30 in v1; 6.7 Mb in v2 vs. 17.1 Mb in v1). Among them, 391 contigs are ordered and oriented (vs. 336 contigs in v1; 99% in v2 vs. 94% in v1). In total, over 80% of the sequence fragments were ordered and oriented, whereas in v1, only ~30% were ordered and oriented. The anchoring (genetic or optical) quality of each contig and substantial physical position changes can be viewed here.

The sequence update was led by Fusheng Wei and Jianwei Zhang at the Arizona Genomics Institute, with contributions from all Consortium members, and David Schwartz's group at the University of Wisconsin [Maize optical map - Shiguo Zhou].

Should you have any questions concerning this new version please contact Rod Wing ( and/or Fusheng Wei ( at the Arizona Genomics Institute and we will address your questions as quickly as possible.

The B73 RefGen_v2 data can be accessed here
The B73 RefGen_v2 is presently being annotated with an expected release date of April 1st, 2010 at