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
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: |
bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA methylation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
organism description > plant > maize
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosome > centromere
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function > chromosome > centromere
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosome
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function > chromosome
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function
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
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > genome annotation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes |
| 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: |
24 Jan 2024 21:10 |
| PMCID: |
PMC8733867 |
| URI: |
https://repository.cshl.edu/id/eprint/40317 |
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