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

Hufford, Matthew B, Seetharam, Arun S, Woodhouse, Margaret R, Chougule, Kapeel M, Ou, Shujun, Liu, Jianing, Ricci, William A, Guo, Tingting, Olson, Andrew, Qiu, Yinjie, Coletta, Rafael Della, Tittes, Silas, Hudson, Asher I, Marand, Alexandre P, Wei, Sharon, Lu, Zhenyuan, Wang, Bo, Tello-Ruiz, Marcela K, Piri, Rebecca D, Wang, Na, Kim, Dong won, Zeng, Yibing, O’Connor, Christine H, Li, Xianran, Gilbert, Amanda M, Baggs, Erin, Krasileva, Ksenia V, Portwood, John L, Cannon, Ethalinda KS, Andorf, Carson M, Manchanda, Nancy, Snodgrass, Samantha J, Hufnagel, David E, Jiang, Qiuhan, Pedersen, Sarah, Syring, Michael L, Kudrna, David A, Llaca, Victor, Fengler, Kevin, Schmitz, Robert J, Ross-Ibarra, Jeffrey, Yu, Jianming, Gent, Jonathan I, Hirsch, Candice N, Ware, Doreen, Dawe, R Kelly (January 2021) De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. bioRxiv. ISSN 2692-8205 (Submitted)

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DOI: 10.1101/2021.01.14.426684

Abstract

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The data indicate that the number of pan-genes 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 reveal 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 overlap QTL and contribute to changes in gene expression.

Item Type:	Paper
Subjects:	organism description > plant > maize organism description > plant
CSHL Authors:	Chougule, Kapeel Olson, Andrew J. Wei, Sharon Lu, Zhenyuan Wang, Bo Ware, Doreen H. Tello-Ruiz, Marcella
Communities:	CSHL labs > Ware lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	16 January 2021
Date Deposited:	13 May 2025 15:51
Last Modified:	13 May 2025 15:51
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41872

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