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 Du; Katherine 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

doi:10.1038/s41588-018-0158-0

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

Biology

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145 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 language	English
Pages (from-to)	1282-1288
Number of pages	7
Journal	Nature Genetics
Volume	50
Issue number	9
DOIs	https://doi.org/10.1038/s41588-018-0158-0
State	Published - 1 Sep 2018

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Springer, N. M., Anderson, S. N., Andorf, C. M., Ahern, K. R., Bai, F., Barad, O., Barbazuk, W. B., Bass, H. W., Baruch, K., Ben-Zvi, G., Buckler, E. S., Bukowski, R., Campbell, M. S., Cannon, E. K. S., Chomet, P., Kelly Dawe, R., Davenport, R., Dooner, H. K., Du, L. H., ... Brutnell, T. P. (2018). The maize w22 genome provides a foundation for functional genomics and transposon biology. Nature Genetics, 50(9), 1282-1288. https://doi.org/10.1038/s41588-018-0158-0

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title = "The maize w22 genome provides a foundation for functional genomics and transposon biology",

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.",

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

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doi = "10.1038/s41588-018-0158-0",

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Springer, NM, Anderson, SN, Andorf, CM, Ahern, KR, Bai, F, Barad, O, Barbazuk, WB, Bass, HW, Baruch, K, Ben-Zvi, G, Buckler, ES, Bukowski, R, Campbell, MS, Cannon, EKS, Chomet, P, Kelly Dawe, R, Davenport, R, Dooner, HK, Du, LH, Du, C, Easterling, KA, Gault, C, Guan, JC, Hunter, CT, Jander, G, Jiao, Y, Koch, KE, Kol, G, Köllner, TG, Kudo, T, Li, Q, Lu, F, Mayfield-Jones, D, Mei, W, McCarty, DR, Noshay, JM, Portwood, JL, Ronen, G, Settles, AM, Shem-Tov, D, Shi, J, Soifer, I, Stein, JC, Stitzer, MC, Suzuki, M, Vera, DL, Vollbrecht, E, Vrebalov, JT, Ware, D, Wei, S, Wimalanathan, K, Woodhouse, MR, Xiong, W & Brutnell, TP 2018, 'The maize w22 genome provides a foundation for functional genomics and transposon biology', Nature Genetics, vol. 50, no. 9, pp. 1282-1288. https://doi.org/10.1038/s41588-018-0158-0

TY - JOUR

T1 - The maize w22 genome provides a foundation for functional genomics and transposon biology

AU - Springer, Nathan M.

AU - Anderson, Sarah N.

AU - Andorf, Carson M.

AU - Ahern, Kevin R.

AU - Bai, Fang

AU - Barad, Omer

AU - Barbazuk, W. Brad

AU - Bass, Hank W.

AU - Baruch, Kobi

AU - Ben-Zvi, Gil

AU - Buckler, Edward S.

AU - Bukowski, Robert

AU - Campbell, Michael S.

AU - Cannon, Ethalinda K.S.

AU - Chomet, Paul

AU - Kelly Dawe, R.

AU - Davenport, Ruth

AU - Dooner, Hugo K.

AU - Du, Limei He

AU - Du, Chunguang

AU - Easterling, Katherine A.

AU - Gault, Christine

AU - Guan, Jiahn Chou

AU - Hunter, Charles T.

AU - Jander, Georg

AU - Jiao, Yinping

AU - Koch, Karen E.

AU - Kol, Guy

AU - Köllner, Tobias G.

AU - Kudo, Toru

AU - Li, Qing

AU - Lu, Fei

AU - Mayfield-Jones, Dustin

AU - Mei, Wenbin

AU - McCarty, Donald R.

AU - Noshay, Jaclyn M.

AU - Portwood, John L.

AU - Ronen, Gil

AU - Settles, A. Mark

AU - Shem-Tov, Doron

AU - Shi, Jinghua

AU - Soifer, Ilya

AU - Stein, Joshua C.

AU - Stitzer, Michelle C.

AU - Suzuki, Masaharu

AU - Vera, Daniel L.

AU - Vollbrecht, Erik

AU - Vrebalov, Julia T.

AU - Ware, Doreen

AU - Wei, Sharon

AU - Wimalanathan, Kokulapalan

AU - Woodhouse, Margaret R.

AU - Xiong, Wenwei

AU - Brutnell, Thomas P.

PY - 2018/9/1

Y1 - 2018/9/1

N2 - 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.

AB - 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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U2 - 10.1038/s41588-018-0158-0

DO - 10.1038/s41588-018-0158-0

M3 - Article

C2 - 30061736

AN - SCOPUS:85051136928

SN - 1061-4036

VL - 50

SP - 1282

EP - 1288

JO - Nature Genetics

JF - Nature Genetics

IS - 9

ER -

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

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