Announcement from the Consortium for Maize Genomics

[Whitelaw, Cathy A.]

Dear Colleagues,

 

The Consortium for Maize Genomics is pleased to announce the release of data
and analysis from the second assembly of ~200,000 methylation-filtered (MF)
and High Cot (HC) genomic sequences (Release 2.0) at
http://www.tigr.org/tdb/tgi/maize/ <http://www.tigr.org/tdb/tgi/maize/> .  

 

Release 2.0 comprises four assemblies: (1) MF-only (Release2.0MF), (2)
HC-only (Release2.0HC), (3) MF and HC combined (Release2.0ALL), (4)
"Unfiltered" (UF) -only (random shotgun reads generated from an unfiltered
maize genomic library) (Release2.0UF).

 

For Release 2.0 assembly statistics summary, please visit:
http://www.tigr.org/tdb/tgi/maize/release2.0/assembly_summary.shtml
<http://www.tigr.org/tdb/tgi/maize/release2.0/assembly_summary.shtml> 

 

For Sequencing progress to date, please visit:

http://www.tigr.org/tdb/tgi/maize/progress_graph.shtml
<http://www.tigr.org/tdb/tgi/maize/progress_graph.shtml> 

 

For Analysis of repetitive sequences in the maize genomic assemblies, please
visit: http://www.tigr.org/tdb/tgi/maize/release2.0/repeat_analysis.shtml
<http://www.tigr.org/tdb/tgi/maize/release2.0/repeat_analysis.shtml> 

 

For Gene matches to maize genomic sequences, please visit:

http://www.tigr.org/tdb/tgi/maize/release2.0/gene_matches.shtml
<http://www.tigr.org/tdb/tgi/maize/release2.0/gene_matches.shtml> 

 

For Mapping maize assemblies to maize sequence markers, please visit:

http://www.tigr.org/tigr-scripts/tgi/marker2.annotator.pl?species=combo_mark
er
<http://www.tigr.org/tigr-scripts/tgi/marker2.annotator.pl?species=combo_mar
ker> 

 

In addition to the Release 2.0 data and BLAST server, we have added several
new features to our website:

 

---GENOME MAP BROWSER---

We have extended the 'Mapping maize assemblies to maize sequence markers'
page to include a genome map browser which allows the user to take a closer
look at specific chromosomal regions or 'bins'.  The genome map browser
provides links between maize sequence markers, maize tentative consensus
(TC) sequences from the TIGR Maize Gene Index
(http://www.tigr.org/tdb/tgi/zmgi/ <http://www.tigr.org/tdb/tgi/zmgi/> ),
maize genomic assemblies (AZMs for Assembled Zea mays) and maize BAC
contigs.  The genome map browser is located at:
http://www.tigr.org/tigr-scripts/tgi/print_chromosomes.pl
<http://www.tigr.org/tigr-scripts/tgi/print_chromosomes.pl> 

and was built using tools provided by the Generic Model Organism Database
Project (http://www.gmod.org/).

 

---BAC VIEWER---

We took all maize genomic sequences >10 kb from GenBank and searched against
our maize AZMs using BLAT.  In the BAC viewer the user can select specific
genomic sequences by accession number and view the alignments of maize AZMs,
annotated repetitive regions and maize, rice and sorghum TC sequences.  The
BAC viewer is located at
http://www.tigr.org/tigr-scripts/tgi/BAC.annotator.pl
<http://www.tigr.org/tigr-scripts/tgi/BAC.annotator.pl>  and was built using
tools provided by the Generic Model Organism Database Project
(http://www.gmod.org/).

 

---BAC ANNOTATION---

We took all maize genomic sequences > 10 kb from GenBank and processed them
using the Eukaryotic Genome Control automated annotation pipeline at TIGR.
The annotation results are available at:
http://www.tigr.org/tigr-scripts/tgi/mz_egc_bac_annot.pl?project=maize
<http://www.tigr.org/tigr-scripts/tgi/mz_egc_bac_annot.pl?project=maize&data
=BAC> &data=BAC.  We provide links to the predicted genes, and include
evidence supporting the gene structure predictions as well as an annotation
report for each individual sequence.

 

---MAIZE REPEAT DATABASE---

We have compiled a database of maize repetitive sequences which is available
for download.  Please visit the following link for more information:
http://www.tigr.org/tdb/tgi/maize/repeat_db.shtml 

 

---GENE ONTOLOGY ASSIGNMENTS---

We have made automated Gene Ontology assignments to the AZMs from the MF and
HC combined assembly, based on significant hits to proteins with an existing
GO assignment.

http://www.tigr.org/tdb/tgi/maize/release2.0/GO/GO.html

 

 

In conjunction with the "Sequencing the Maize Genome" project we have
created a website for the general public (www.maizegenome.org
<http://www.maizegenome.org/> ) which aims to provide information and
updates relating to active maize genome sequencing projects.  

 

 

We are constantly searching for ways to improve our websites and to make the
data generated by this project easily accessible and informative to the
maize research community. As always, we welcome your feedback -- please
e-mail us at  http://www.tigr.org/tdb/tgi/maize/ .

 

 

Cathy Whitelaw (The Institute for Genomic Research)

Brad Barbazuk (Donald Danforth Plant Science Center)

 

This project is supported by NSF Plant Genome award, DBI-0221536 

 

 

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