The University of Arizona



Several families of maize gene-enriched sequences have been produced (AZM,EST,MSLL,HMPR), and maize is currently undergoing full BAC-by-BAC sequencing. We download the most current maize BACs from Genbank every night and align the gene-rich sequences to them, in order to elucidate their structure.

This site has been funded in part by NSF grant #0321724

Reference: Nelson, W., Luo, M., Ma, J., Haller, K., Bharti, A., Messing, J., Wing, R., San Miguel, P., Bennetzen, J., and Soderlund, C. (2008) Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains. BMC Genomics, 9:621doi:10.1186/1471-2164-9-621. Link


Site Functions
Mini-BACs A table of images showing the gene evidence for each BAC, with links to the genome browser.
Order Many of the clones for the gene rich sequences may be ordered.
Site Functions Information
Mini-BACs: A table of images that show a birds-eye view of MSLL and HMPR[1], AZMs[2], EST contigs[3], and repeats along the maize BACs[4]. These are updated regularly with new and updated sequenced BACs from Genbank. Each BAC image links to a Genome Browser of the BAC with additional tracks for Methyl-filtered, High-Cot, RescueMU[5], BESs[6], and FGENESH[7] predictions.
Orders: The Arizona Genome Institute provides the clones for MSLL, HMPR, ESTs from the Maize FL-cDNA project, and the MF and HC from the AZM project [2].
References
[1] MSLL and HMPR
Nelson, W., Luo, M., Ma, J., Haller, K., Bharti, A., Messing, J., Wing, R., San Miguel, P., Bennetzen, J., and Soderlund, C. (2008) Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains. BMC Genomics 2008, 9:621doi:10.1186/1471-2164-9-621
[2] Assembled Zea Mays (Methyl-Filtered and High Cot sequence)
Whitelaw, C.A., Barbazuk, W.B., Pertea, G., Chan, A.P., Cheung, F., Lee, Y., Zheng, L., van Heering en, S., Karamycheva, S., Bennetzen, J.L., SanMiguel, P., Lakey, N., Bedell, J., Yuan, Y., Budiman, M.A., Resnick, A., Van Aken, S., Utterback, T., Riedmuller, S., Williams, M., Feldblyum, T., Schubert, K., Beachy, R., Fraser, C.M., and Quackenbush, J. (2003). Enrichment of gene-coding sequences in maize by genome filtration. Science 302, 2118-2120.
[3] Maize FL-cDNA Project
[4] Maize Sequencing Project
[5] Fernandes, J., Dong, Q., Schneider, B., Morrow, D., Nan, G., Brendel, V., and Walbot, V. (2004). Genome-wide mutagenesis of Zea mays L. using RescueMu transposons. Genome Biology 5: R82.
[6] Maize BES sequences
Messing, J., Bharti, A.K., Karlowski, W.M., Gundlach, H., Kim, H.R., Yu, Y., Wei, F., Fuks, G., Soderlund, C., Mayer, K.F.X. and Wing, R.A. (2004) Sequence composition and genome organization of maize. Proc. Natl. Acad. Sci. USA 101: 14349-14354.
[7] Fgenesh gene finding program (Salamov and Solovyev)
Last Modified: 5 July 07

Last Modified Thursday October 11, 2012 08:59 AM and 22 seconds