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

Matthew B. Hufford, View ORCID ProfileArun S. Seetharam, Margaret R. Woodhouse, Kapeel M. Chougule, View ORCID ProfileShujun Ou, Jianing Liu, William A. Ricci, Tingting Guo, Andrew Olson, View ORCID ProfileYinjie Qiu, Rafael Della Coletta, Silas Tittes, Asher I. Hudson, View ORCID ProfileAlexandre P. Marand, Sharon Wei, Zhenyuan Lu, Bo Wang, Marcela K. Tello-Ruiz, Rebecca D. Piri, Na Wang, Dong won Kim, Yibing Zeng, Christine H. O’Connor, Xianran Li, Amanda M. Gilbert, Erin Baggs, Ksenia V. Krasileva, John L. Portwood II, View ORCID ProfileEthalinda K.S. Cannon, Carson M. Andorf, Nancy Manchanda, Samantha J. Snodgrass, David E. Hufnagel, Qiuhan Jiang, Sarah Pedersen, Michael L. Syring, David A. Kudrna, Victor Llaca, Kevin Fengler, Robert J. Schmitz, Jeffrey Ross-Ibarra, Jianming Yu, Jonathan I. Gent, Candice N. Hirsch, Doreen Ware, R. Kelly Dawe
doi: https://doi.org/10.1101/2021.01.14.426684
Matthew B. Hufford
1Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011
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Arun S. Seetharam
1Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011
2Genome Informatics Facility, Iowa State University, Ames, IA 50011
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  • ORCID record for Arun S. Seetharam
Margaret R. Woodhouse
3USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011
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Kapeel M. Chougule
4Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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Shujun Ou
1Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011
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Jianing Liu
5Department of Genetics, University of Georgia, Athens, GA 30602
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William A. Ricci
6Department of Plant Biology, University of Georgia, Athens, GA 30602
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Tingting Guo
8Department of Agronomy, Iowa State University, Ames, IA 50011
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Andrew Olson
4Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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Yinjie Qiu
9Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
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  • ORCID record for Yinjie Qiu
Rafael Della Coletta
9Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
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Silas Tittes
10Center for Population Biology, University of California, Davis, CA 95616
11Department of Evolution and Ecology, University of California, Davis, CA 95616
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Asher I. Hudson
10Center for Population Biology, University of California, Davis, CA 95616
11Department of Evolution and Ecology, University of California, Davis, CA 95616
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Alexandre P. Marand
5Department of Genetics, University of Georgia, Athens, GA 30602
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Sharon Wei
4Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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Zhenyuan Lu
4Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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Bo Wang
4Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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Marcela K. Tello-Ruiz
4Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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Rebecca D. Piri
7Institute of Bioinformatics, University of Georgia, Athens, GA 30602
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Na Wang
6Department of Plant Biology, University of Georgia, Athens, GA 30602
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Dong won Kim
6Department of Plant Biology, University of Georgia, Athens, GA 30602
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Yibing Zeng
5Department of Genetics, University of Georgia, Athens, GA 30602
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Christine H. O’Connor
9Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
12Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108
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Xianran Li
8Department of Agronomy, Iowa State University, Ames, IA 50011
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Amanda M. Gilbert
9Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
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Erin Baggs
13Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
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Ksenia V. Krasileva
13Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
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John L. Portwood II
3USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011
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Ethalinda K.S. Cannon
3USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011
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  • ORCID record for Ethalinda K.S. Cannon
Carson M. Andorf
3USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011
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Nancy Manchanda
1Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011
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Samantha J. Snodgrass
1Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011
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David E. Hufnagel
1Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011
14Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010
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Qiuhan Jiang
1Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011
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Sarah Pedersen
1Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011
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Michael L. Syring
1Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011
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David A. Kudrna
15Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721
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Victor Llaca
16Corteva Agriscience, Johnston, IA 50131
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Kevin Fengler
16Corteva Agriscience, Johnston, IA 50131
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Robert J. Schmitz
5Department of Genetics, University of Georgia, Athens, GA 30602
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Jeffrey Ross-Ibarra
9Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
11Department of Evolution and Ecology, University of California, Davis, CA 95616
17Genome Center, University of California, Davis, CA 95616
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Jianming Yu
8Department of Agronomy, Iowa State University, Ames, IA 50011
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Jonathan I. Gent
6Department of Plant Biology, University of Georgia, Athens, GA 30602
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Candice N. Hirsch
9Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
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Doreen Ware
4Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
18USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853
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R. Kelly Dawe
5Department of Genetics, University of Georgia, Athens, GA 30602
6Department of Plant Biology, University of Georgia, Athens, GA 30602
7Institute of Bioinformatics, University of Georgia, Athens, GA 30602
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  • For correspondence: kdawe@uga.edu
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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.

One sentence summary A multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation.

Competing Interest Statement

RJS is a co-founder of REquest Genomics, LLC, a company that provides epigenomic services. All other authors declare no competing interests.

Footnotes

  • https://github.com/HuffordLab/NAM-genomes

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.
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De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
Matthew B. Hufford, Arun S. Seetharam, Margaret R. Woodhouse, Kapeel M. Chougule, Shujun Ou, Jianing Liu, William A. Ricci, Tingting Guo, Andrew Olson, Yinjie Qiu, Rafael Della Coletta, Silas Tittes, Asher I. Hudson, Alexandre P. Marand, Sharon Wei, Zhenyuan Lu, Bo Wang, Marcela K. Tello-Ruiz, Rebecca D. Piri, Na Wang, Dong won Kim, Yibing Zeng, Christine H. O’Connor, Xianran Li, Amanda M. Gilbert, Erin Baggs, Ksenia V. Krasileva, John L. Portwood II, Ethalinda K.S. Cannon, Carson M. Andorf, Nancy Manchanda, Samantha J. Snodgrass, David E. Hufnagel, Qiuhan Jiang, Sarah Pedersen, Michael L. Syring, David A. Kudrna, Victor Llaca, Kevin Fengler, Robert J. Schmitz, Jeffrey Ross-Ibarra, Jianming Yu, Jonathan I. Gent, Candice N. Hirsch, Doreen Ware, R. Kelly Dawe
bioRxiv 2021.01.14.426684; doi: https://doi.org/10.1101/2021.01.14.426684
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De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
Matthew B. Hufford, Arun S. Seetharam, Margaret R. Woodhouse, Kapeel M. Chougule, Shujun Ou, Jianing Liu, William A. Ricci, Tingting Guo, Andrew Olson, Yinjie Qiu, Rafael Della Coletta, Silas Tittes, Asher I. Hudson, Alexandre P. Marand, Sharon Wei, Zhenyuan Lu, Bo Wang, Marcela K. Tello-Ruiz, Rebecca D. Piri, Na Wang, Dong won Kim, Yibing Zeng, Christine H. O’Connor, Xianran Li, Amanda M. Gilbert, Erin Baggs, Ksenia V. Krasileva, John L. Portwood II, Ethalinda K.S. Cannon, Carson M. Andorf, Nancy Manchanda, Samantha J. Snodgrass, David E. Hufnagel, Qiuhan Jiang, Sarah Pedersen, Michael L. Syring, David A. Kudrna, Victor Llaca, Kevin Fengler, Robert J. Schmitz, Jeffrey Ross-Ibarra, Jianming Yu, Jonathan I. Gent, Candice N. Hirsch, Doreen Ware, R. Kelly Dawe
bioRxiv 2021.01.14.426684; doi: https://doi.org/10.1101/2021.01.14.426684

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