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. 2006 Jan 1;34(Database issue):D771-6.
doi: 10.1093/nar/gkj072.

The TIGR Maize Database

Agnes P Chan  1 , Geo Pertea, Foo Cheung, Dan Lee, Li Zheng, Cathy Whitelaw, Ana C Pontaroli, Phillip SanMiguel, Yinan Yuan, Jeffrey Bennetzen, William Brad Barbazuk, John Quackenbush, Pablo D Rabinowicz
Affiliations

The TIGR Maize Database

Agnes P Chan et al. Nucleic Acids Res. .

Abstract

Maize is a staple crop of the grass family and also an excellent model for plant genetics. Owing to the large size and repetitiveness of its genome, we previously investigated two approaches to accelerate gene discovery and genome analysis in maize: methylation filtration and high C(0)t selection. These techniques allow the construction of gene-enriched genomic libraries by minimizing repeat sequences due to either their methylation status or their copy number, yielding a 7-fold enrichment in genic sequences relative to a random genomic library. Approximately 900,000 gene-enriched reads from maize were generated and clustered into Assembled Zea mays (AZM) sequences. Here we report the current AZM release, which consists of approximately 298 Mb representing 243,807 sequence assemblies and singletons. In order to provide a repository of publicly available maize genomic sequences, we have created the TIGR Maize Database (http://maize.tigr.org). In this resource, we have assembled and annotated the AZMs and used available sequenced markers to anchor AZMs to maize chromosomes. We have constructed a maize repeat database and generated draft sequence assemblies of 287 maize bacterial artificial chromosome (BAC) clone sequences, which we annotated along with 172 additional publicly available BAC clones. All sequences, assemblies and annotations are available at the project website via web interfaces and FTP downloads.

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Figures

Figure 1
Figure 1
An AZM assembly report showing the assembled consensus sequence, a graphical layout of the component reads and related protein hits.
Figure 2
Figure 2
In silico alignments of AZMs to maize chromosomes through sequenced genetic markers. (A) A section of a genome view displaying AZMs anchored to individual chromosomes through alignments to genetic markers. (B) Mapping AZM assemblies to genetic markers. In both displays, the AZM to marker mappings can be selected by chromosome, AZM accessions, genetic loci or genetic marker accessions.
See this image and copyright information in PMC

References

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