De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Authors: HUFFORD, MATTHEW - Iowa State University; SEETHARAM, ARUN - Iowa State University; Woodhouse, Margaret; CHOUGLE, KAPEEL - Cold Spring Harbor Laboratory; OU, SHUJUN - Iowa State University; LIU, JIANING - University Of Georgia; RICCI, WILLIAM - University Of Georgia; GUO, TINGTING - University Of Georgia; OLSON, ANDREW - Cold Spring Harbor Laboratory; QIU, YINGJIE - University Of Minnesota; Portwood, John; Cannon, Ethalinda; Andorf, Carson; Ware, Doreen; DAWE, KELLY - University Of Georgia

Submitted to: Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/24/2021
Publication Date: 8/6/2021
Citation: Hufford, M.B., Seetharam, A.S., Woodhouse, M.H., Chougle, K.M., Ou, S., Liu, J., Ricci, W.A., Guo, T., Olson, A., Qiu, Y., Portwood II, J.L., Cannon, E.K., Andorf, C.M., Ware, D., Dawe, K.R. et al. 2021. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science. 373(6555):655-662. https://doi.org/10.1126/science.abg5289.
DOI: https://doi.org/10.1126/science.abg5289

Interpretive Summary: We report the genome sequencing and assembly of 26 maize (corn) cultivars that represent the diversity of domesticated maize. These 26 cultivars have used by corn researchers for years to study corn development, disease resistance, and other crop improvement-related features. The high-quality genome assemblies of these cultivars, along with their gene and functional information derived from this study, will allow researchers to better understand the structural and functional diversity of the maize genome across the species, leading to future crop improvement.

Technical Abstract: We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 maize inbreds that serve as the founders for the maize nested association mapping population. The data indicate that the number of pan-genes in maize exceeds 103,000 and that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres further revealed the locations and internal structures of major cytological landmarks. We show that combining structural variation with SNPs can improve the power of quantitative mapping studies. Finally, we document variation at the level of DNA methylation, and demonstrate that unmethylated regions are enriched for cis-regulatory elements that correlate with known QTLs and changes in gene expression.