Journal Article

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

Hunter, Charles T., Li, Qing, Noshay, Jaclyn M., Springer, Nathan M., Wimalanathan, Kokulapalan, Jiao, Yinping, Suzuki, Masaharu, Vrebalov, Julia T., Lu, Fei, Easterling, Katherine A., McCarty, Donald R., Shi, Jinghua, Woodhouse, Margaret R., Jander, Georg, Xiong, Wenwei, Ronen, Gil, Anderson, Sarah N., Bass, Hank W., Köllner, Tobias G., Guan, Jiahn-Chou, Mayfield-Jones, Dustin, Wei, Sharon, Vollbrecht, Erik, Baruch, Kobi, Vera, Daniel L., Ware, Doreen, Brutnell, Thomas P., Bukowski, Robert, Campbell, Michael S., Koch, Karen E., Shem-Tov, Doron, Stitzer, Michelle C., Gault, Christine, Dooner, Hugo K., Davenport, Ruth, Andorf, Carson M., Ahern, Kevin R., Stein, Joshua C., Kol, Guy, Du, Limei He, Mei, Wenbin, Ben-Zvi, Gil, Chomet, Paul, Du, Chunguang, Portwood, John L., Bai, Fang, Settles, A. Mark, Dawe, R. Kelly, Barbazuk, W. Brad, Buckler, Edward S., Kudo, Toru, Cannon, Ethalinda K. S., Barad, Omer, Soifer, Ilya

2018

Overview

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. Sequencing and de novo assembly of the maize W22 reference genome enable accurate placement of Mutator ( Mu ) and Dissociation ( Ds ) transposable element insertions, providing a foundation for maize functional genomics and transposon biology.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 45 / 45/23 / 45/70 / 631/208/176 / 631/208/191/1908 / 631/208/212 / 631/208/514/1948 / 631/449/2491 / Agriculture / Animal Genetics and Genomics / Annotations / Bioinformatics / Biomedical and Life Sciences / Biomedicine / Bisulfite / Cancer Research / Chromatin / Copy number / Corn / Criminal investigation / Deoxyribonucleic acid / DNA / DNA methylation / DNA sequencing / Domestication / Gene Function / Genes / Genetic aspects / Genetic polymorphisms / Genetic research / Genetics / Genomes / Genomics / Heterogeneity / Human Genetics / Inbreeding / Methylation / Nuclease / Open reading frames / Quality control / Ribonucleic acid / RNA / Sensitivity analysis / Single nucleotide polymorphisms / Single-nucleotide polymorphism / Sulfites / Transposons