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  The maize W22 genome provides a foundation for functional genomics and transposon biology

Springer, N. M., Anderson, S. N., Andorf, C. M., Ahern, K. R., Bai, F., Barad, O., et al. (2018). The maize W22 genome provides a foundation for functional genomics and transposon biology. Nature Genetics, 50, 1282-1288. doi:10.1038/s41588-018-0158-0.

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Springer, Nathan M., Author
Anderson, Sarah N., Author
Andorf, Carson M., Author
Ahern, Kevin R., Author
Bai, Fang, Author
Barad, Omer, Author
Barbazuk, W. Brad, Author
Bass, Hank W., Author
Baruch, Kobi, Author
Ben-Zvi, Gil, Author
Buckler, Edward S., Author
Bukowski, Robert, Author
Campbell, Michael S., Author
Cannon, Ethalinda K. S., Author
Chomet, Paul, Author
Dawe, R. Kelly, Author
Davenport, Ruth, Author
Dooner, Hugo K., Author
Du, Limei He, Author
Du, Chunguang, Author
Easterling, Katherine A., AuthorGault, Christine, AuthorGuan, Jiahn-Chou, AuthorHunter, Charles T., AuthorJander, Georg, AuthorJiao, Yinping, AuthorKoch, Karen E., AuthorKol, Guy, AuthorKöllner, Tobias G.1, Author           Kudo, Toru, AuthorLi, Qing, AuthorLu, Fei, AuthorMayfield-Jones, Dustin, AuthorMei, Wenbin, AuthorMcCarty, Donald R., AuthorNoshay, Jaclyn M., AuthorII, John L. Portwood, AuthorRonen, Gil, AuthorSettles, A. Mark, AuthorShem-Tov, Doron, AuthorShi, Jinghua, AuthorSoifer, Ilya, AuthorStein, Joshua C., AuthorStitzer, Michelle C., AuthorSuzuki, Masaharu, AuthorVera, Daniel L., AuthorVollbrecht, Erik, AuthorVrebalov, Julia T., AuthorWare, Doreen, AuthorWei, Sharon, AuthorWimalanathan, Kokulapalan, AuthorWoodhouse, Margaret R., AuthorXiong, Wenwei, AuthorBrutnell, Thomas P., Author more..
Affiliations:
1Department of Biochemistry, Prof. J. Gershenzon, MPI for Chemical Ecology, Max Planck Society, ou_421893              

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 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.

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 Dates: 2018-05-172018-07-302018-08
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: Other: GER512
DOI: 10.1038/s41588-018-0158-0
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Title: Nature Genetics
  Other : Nature Genet.
Source Genre: Journal
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Publ. Info: New York, NY : Nature America, Inc.
Pages: - Volume / Issue: 50 Sequence Number: - Start / End Page: 1282 - 1288 Identifier: ISSN: 1061-4036
CoNE: https://pure.mpg.de/cone/journals/resource/954925598609