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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #327220

Research Project: MaizeGDB: Enabling Access to Basic, Translational, and Applied Research Information

Location: Corn Insects and Crop Genetics Research

Title: Sequence, assembly and annotation of the maize W22 genome

Author
item Andorf, Carson
item Ahem, Kevin - Cornell University - New York
item Bai, Fang - University Of Florida
item Barad, Omer - Nrgene
item Barbazuk, Brad - University Of Florida
item Bass, Hank - Florida State University
item Baruch, Kobi - Nrgene
item Ben-zvi, Gil - Nrgene
item Buckler, Edward - Ed
item Bukowski, Robert - Cornell University - New York
item Davenport, Ruth - University Of Florida
item Dooner, Hugo - Rutgers University
item He Du, Limei - Rutgers University
item Du, Chunguang - Montclair State University
item Easterling, Katherline - Florida State University
item Gault, Christine - Cornell University - New York
item Guan, Jiahn-chou - University Of Florida
item Jander, Georg - Boyce Thompson Institute
item Jiao, Yingping - Cold Spring Harbor Laboratory
item Koch, Karen - University Of Florida
item Kol, Guy - Nrgene
item Kudo, Toru - University Of Florida
item Li, Qing - University Of Minnesota
item Lu, Fei - Cornell University - New York
item Mayfield-jones, Dustin - Danforth Plant Science Center
item Mei, Wenbin - University Of Florida
item Mccarty, Don - University Of Florida
item Portwood, John
item Ronen, Gil - Nrgene
item Settles, Mark - University Of Florida
item Shem-tov, Doron - Nrgene
item Soifer, Ilya - Nrgene
item Springer, Nathan - University Of Minnesota
item Suzuki, Masaharu - University Of Florida
item Vera, Daniel - Florida State University
item Vollbrecht, Erik - Iowa State University
item Vrebalov, Julia - Boyce Thompson Institute
item Ware, Doreen
item Wimalanathan, Kokulapalan - Iowa State University
item Xiong, Wenwei - Montclair State University
item Brutnell, Thomas - Danforth Plant Science Center

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/16/2016
Publication Date: 3/17/2016
Citation: Andorf, C.M., Ahem, K., Bai, F., Barad, O., Barbazuk, B.W., Bass, H.W., Baruch, K., Ben-Zvi, G., Buckler Iv, E.S., Bukowski, R., Davenport, R., Dooner, H.K., He Du, L., Du, C., Easterling, K.A., Gault, C.M., Guan, J., Jander, G., Jiao, Y., Koch, K., Kol, G., Kudo, T., Li, Q., Lu, F., Mayfield-Jones, D., Mei, W., McCarty, D., Portwood II, J.L., Ronen, G., Settles, M.A., Shem-Tov, D., Soifer, I., Springer, N.M., Suzuki, M., Vera, D., Vollbrecht, E., Vrebalov, J.T., Ware, D., Wimalanathan, K., Xiong, W., Brutnell, T. 2016. Sequence, assembly and annotation of the maize W22 genome. In: 58th Annual Maize Genetics Conference, March 17-20, 2016, Jacksonville, Florida. p. 91.

Interpretive Summary:

Technical Abstract: Since its adoption by Brink and colleagues in the 1950s and 60s, the maize W22 inbred has been utilized extensively to understand fundamental genetic and epigenetic processes such recombination, transposition and paramutation. To maximize the utility of W22 in gene discovery, we have Illumina sequencing technologies and de novo assembled a color-converted W22 reference genome. Significant structural heterogeneity exists in comparisons to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single nucleotide polymorphisms. The generation of this high quality reference genome has enabled the accurate placement of several thousand Mutator and Dissociation transposable elements from community transposon mutagenesis projects that enable the use of both engineered and endogenous elements for reverse and forward genetics in maize. Annotation of the genome has been informed by RNAseq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to fine map open reading frames, open chromatin sites, and DNA methylation profiles, respectively. Several independent assessments of the quality of the genome assembly including comparisons to high resolution genetic maps, Sanger-sequenced regions of high complexity and transposon site insertion mapping coupled with the integration of global epigenetic and gene expression annotation reveal that the W22 genome now represents the highest quality maize reference genome in the public domain.