The maize w22 genome provides a foundation for functional genomics and transposon biology

Nathan M. Springer, Sarah N. Anderson, Carson M. Andorf, Kevin R. Ahern, Fang Bai, Omer Barad, W. Brad Barbazuk, Hank W. Bass, Kobi Baruch, Gil Ben-Zvi, Edward S. Buckler, Robert Bukowski, Michael S. Campbell, Ethalinda K.S. Cannon, Paul Chomet, R. Kelly Dawe, Ruth Davenport, Hugo K. Dooner, Limei He Du, Chunguang DuKatherine A. Easterling, Christine Gault, Jiahn Chou Guan, Charles T. Hunter, Georg Jander, Yinping Jiao, Karen E. Koch, Guy Kol, Tobias G. Köllner, Toru Kudo, Qing Li, Fei Lu, Dustin Mayfield-Jones, Wenbin Mei, Donald R. McCarty, Jaclyn M. Noshay, John L. Portwood, Gil Ronen, A. Mark Settles, Doron Shem-Tov, Jinghua Shi, Ilya Soifer, Joshua C. Stein, Michelle C. Stitzer, Masaharu Suzuki, Daniel L. Vera, Erik Vollbrecht, Julia T. Vrebalov, Doreen Ware, Sharon Wei, Kokulapalan Wimalanathan, Margaret R. Woodhouse, Wenwei Xiong, Thomas P. Brutnell

Research output: Contribution to journalArticlepeer-review

58 Scopus citations

Abstract

The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNA-seq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to map open reading frames, open chromatin sites and DNA methylation profiles, respectively. Collectively, the resources developed here integrate W22 as a community reference genome for functional genomics and provide a foundation for the maize pan-genome.

Original languageEnglish (US)
JournalNature Genetics
Volume50
Issue number9
DOIs
StatePublished - Sep 1 2018

Bibliographical note

Funding Information:
This work was supported by grants from the following: National Science Foundation NSF-MCB 0920218 to H.K.D.; NSF-MCB 1025976 to K.E.K.; NSF-IOS 1031416 to A.M.S.; NSF-IOS 1237931 to N.M.S.; NSF-IOS 1116561 to D.R.M. and K.E.K.; NSF-IOS 1238014 to E.S.B.; NSF-IOS 1314143 to T.P.B. and E.V.; NSF IOS-1339237 and IOS-1139329 to G.J.; NSF MCB-1412218 to A.M.S. and W.B.B.; NSF IOS-1444514 to R.K.D.; NSF-IOS 1521100 to J.-C.G., K.E.K. and D.R.M.; NSF-IOS 1547787 to W.B.B.; NSF Graduate Research Fellowship and University of Florida Graduate Student Fellowship to C.G.; NSF Graduate Research Fellowship DGE-0802270 to C.G.; the United States Department of Agriculture (USDA) in kind to C.M.A., E.K.S.C., M.R.W. and J.L.P.; USDA-ARS 6036-21000-011-00D to C.T.H.; USDA-NIFA 2016-67013-24747 to N.M.S.; USDA-NIFA 2011-67003-30215 to D.R.M. and K.E.K.; USDA-NIFA 2011-67013-30082 to D.R.M. and M.S.; USDA-ARS and the NSF-IOS Plant Genome 1238014 to E.S.B.; the Enterprise Rent-A-Car Institute for Renewable Fuels at the Donald Danforth Plant Science Center to T.P.B.; and the Vasil-Monsanto Endowment to A.M.S. The use of trade names, commercial products or corporations in this publication is for the information and convenience of the reader and does not imply an official recommendation, endorsement or approval by the US Department of Agriculture or the Agricultural Research Service for any product or service to the exclusion of others that may be suitable. USDA is an equal opportunity provider and employer.

Copyright:
Copyright 2019 Elsevier B.V., All rights reserved.

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