Overview

This release of phytozome includes the 5b.60 annotation (unfiltered working set) of the maize "B73" genome v2 produced by the Maize Genome Project, and the alignment of "Mo17" 454 reads to this reference sequence.

The browser displays:

1. Gene structure predictions from the 5a.59 working set of maizesequence.org (see below)
2. Alignments of maize ESTs from genbank
3. Alignment of grass transcript assemblies (i.e., assemblies of ESTs) from PlantTA
4. Alignment of 454 shotgun reads from the Mo17 project

Important note on data sources

The B73 assembly used in the 5b.60 annation release is Maize Golden Path B73 RefGen_v2. The first draft of the maize genome sequence assembly. Developed by Wing and Wei et al of Arizona Genomics Institute and released on March 8, 2010. More information can be found at maizesequence.org.

Please consult www.maizesequence.org for more details about this release and future plans.

For more information on the B73 Maize Genome Project, please see www.maizesequence.org/overview.html.

Please note that the B73 assembly and annotation used here are subject to the "Data Use Policy" of the Maize Genome Project, reproduced here:

Our goal is to provide high quality sequence information to the research community in a timely manner. Accordingly, individual sequence read traces are submitted to the NCBI Trace Archive as soon as they have exited our quality control pipeline. Whole genome sequence assemblies are released as soon as possible following appropriate quality analysis. Our archive site contains draft versions of the genome sequence assemblies, and we ask that you understand that these represent preliminary data, subject to omissions and errors. In addition, whole genome assemblies are likely to change upon the availability of new data, and our website will document new assembly versions as they are released.

In recognition of the extensive effort that underlies these genome sequencing projects, we ask that you appropriately acknowledge the use of any preliminary data. We offer the following example for acknowledgement: "These data were produced by the Genome Sequencing Center at Washington University School of Medicine in St. Louis and can be obtained from ftp://genome.wustl.edu/pub/xxx", where xxx refers to the appropriate ftp directory from which the data has been obtained. Our official web address may also be used. This recommendation is in accordance with the adopted guidelines by the genome sequencing community in a statement of principles for the distribution and use of large-scale sequencing data: Community Resource Projects and the resulting NHGRI policy statement. If you have any questions regarding the use of this data, please contact us at web address: webmaster@genome.wustl.edu . We request that you contact the Director of the Sequencing Center, Richard Wilson, before publishing analyses of the sequence on a chromosome or genome scale. We welcome collaborative interaction to provide the community with improved whole genome analyses and annotations.

Other tracks on the Phytozome maize B73 browser are:

1. "Repeats" is repeat-masked region in the masked genome provided by Cold Spring Harbor
2. Zea mays ESTs from Genbank, aligned using the Program to Assembly Spliced Alignments (PASA, Haas et al.)
3. Zea mays "transcript assemblies" (i.e., assembled ESTs) obtained from the PlantTA project (plantta.jcvi.org/)
4. Alignment of peptides from other plants in the Phytozome database (including sorghum, rice, and Brachypodium), using BLATX (Kent)
5. Alignment of 454 shotgun reads from Mo17. "selected" reads are 16M reads with less than 1/3 of their length masked. These are aligned to the unmasked genome. The "65M" set is a the full ~10x Mo17 shotgun dataset, aligned to the hard-masked genome. Note that only the longest aligning stretch is shown; these alignments terminate either at the end of a read or at a masked position.