What's New in Release 4a.53

Release of an improved version of the B73 genome assembly
Dear Maize Collaborators,

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 (rwing@ag.arizona.edu) and/or Fusheng Wei (fushengw@ag.arizona.edu) 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 http://maizesequence.org.
MaizeSequence.org Release 4a.53!
After several obstacles, we are proud to present Release 4a.53 of the maize genome browser. Apart from sporting a new look, the genome browser now presents the first version of the maize genome assembly.
New data sets
We are now providing various useful data sets from collaborators. For more information, see the collaborator page
Science publication of the maize genome
On November 20, 2009, Science published the maize genome paper, titled, The B73 Maize Genome: Complexity, Diversity, and Dynamics. Alongside the main paper, 3 companion papers were published in Science and 10 companion papers were published in PLoS Genetics. The papers represent the culmination of the four-year project and the hard work of countless individuals. Congratulations to all who contributed. [USDA press release]
Array mapping environment
Ensembl Functional Genomics has a new improved array-mapping environment, integrating genomic and cdna mapping, extendable array format configuration, support for multi-species databases and improved probe-to-transcript annotation.
SG: DAS support in eFG environment
DAS functions are now available in the eFG environment to support easy setup and administration of DAS tracks.
Core schema changes
The external_db table has had its 'type' column changed to include 'Ensembl' as a value in the enum array; this is to accommodate changes in eFG. Also the identity_xref fields have been renamed to 'ensembl' and 'xref', replacing 'query', 'target', 'hit' and 'translation'.
Compara schema changes
A new table called 'constrained_element' has been added to replace genomic_align_block and genomic_align for constrained elements.
Changes to allow stable_ids for ensembl families:
1. 'family' table is going to get a new 'version' column for its' stable_ids.
2. 'protein_tree_stable_id' table is introduced to give stable_ids to the protein trees.
3. 'mapping_session' and 'stable_id_history' tables are introduced to track the stable_ids between releases.
A couple of text fields have been changed to enums for efficiency/speed.
API bug fix
A bug has been fixed in the Ensembl Core API (TranscriptAdaptor.pm) that prevented selenocysteines from being properly translated into 'U'. This bug was fixed in the later stages of the Ensembl release cycle, which means that, for a small number of transcripts, there will be a difference in translated sequence when comparing the fasta protein dumps with what the Ensembl Core API reports.

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