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, Della Coletta, Rafael, 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 (August 2021) De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science, 373 (6555). pp. 655-662. ISSN 0036-8075

URL: https://www.ncbi.nlm.nih.gov/pubmed/34353948
DOI: 10.1126/science.abg5289

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 number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate 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 revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.

Item Type: Paper
Subjects: organism description > plant > maize
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > comparative genomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > de novo assembly
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > genome annotation
CSHL Authors:
Communities: CSHL labs > Ware lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 6 August 2021
Date Deposited: 11 Aug 2021 13:37
Last Modified: 11 Aug 2021 13:37
URI: https://repository.cshl.edu/id/eprint/40317

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