The maize W22 genome provides a foundation for functional genomics and transposon biology

Springer, N. M., Anderson, S. N., Andorf, C. M., Ahern, K. R., Bai, F., Barad, O., Barbazuk, W. B., Bass, H. W., Baruch, K., Ben-Zvi, G., Buckler, E. S., Bukowski, R., Campbell, M. S., Cannon, E. K. S., Chomet, P., Dawe, R. K., Davenport, R., Dooner, H. K., Du, L. H., Du, C., Easterling, K. A., Gault, C., Guan, J. C., Hunter, C. T., Jander, G., Jiao, Y., Koch, K. E., Kol, G., Kollner, T. G., Kudo, T., Li, Q., Lu, F., Mayfield-Jones, D., Mei, W., McCarty, D. R., Noshay, J. M., Portwood, J. L., Ronen, G., Settles, A. M., Shem-Tov, D., Shi, J., Soifer, I., Stein, J. C., Stitzer, M. C., Suzuki, M., Vera, D. L., Vollbrecht, E., Vrebalov, J. T., Ware, D., Wei, S., Wimalanathan, K., Woodhouse, M. R., Xiong, W., Brutnell, T. P. (2018) The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat Genet. ISSN 1061-4036

URL: https://www.ncbi.nlm.nih.gov/pubmed/30061736
DOI: 10.1038/s41588-018-0158-0

Abstract

The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNA-seq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to map open reading frames, open chromatin sites and DNA methylation profiles, respectively. Collectively, the resources developed here integrate W22 as a community reference genome for functional genomics and provide a foundation for the maize pan-genome.

Item Type: Paper
Subjects: organism description > plant > maize
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transposons
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Ware lab
Depositing User: Matthew Dunn
Date Deposited: 14 Aug 2018 15:13
Last Modified: 14 Aug 2018 15:13
Related URLs:
URI: http://repository.cshl.edu/id/eprint/37130

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