Metadata for assembly Zm-W22-REFERENCE-NRGENE-2.0

Project: W22 (C1:R-r:std - PI 674445) Sequence and Assembly
BioProject: PRJNA311133
Stock provided by Hugo Dooner. This stock was derived by R.A. Brink at the U. of Wisconsin for his studies on paramutation at the R locus by five back-crosses of the regular W22 inbred (colorless seed because of c1; r alleles) to a purple seed stock that he apparently obtained from Cornell (Brink, 1956, Genetics 41:872-889). This resulted in the introgression of C1 and R alleles from the purple stock into W22. The C1 allele was characterized by Karen Cone. The R allele is the paramutable R-r: standard allele (Brink, 1956, op. cit.; Dooner & Kermicle, 1971, Genetics 67:427-436). Allele was obtained in 1972 from the U. of Wisconsin cold storage collection (pedigree CS-810) and has been selfed for 30 generations. Known alleles of color genes:  C1 (Cooper and Cone, unpub.; GenBank AF320614); R-r: std (Walker et al., 1995, EMBO J. 10: 2360-2363; only partial sequence); Bz1-W22 (Dooner & He, 2008, Plant Cell 20:249-258; GenBank EU338354).

BioSample: SAMN04479043

Assembly and sequencing:
<u>Assembly methods:</u> DenovoMAGIC<br><u>Construction of pseudomolecules:</u> Scaffolds were ordered and oriented
<u>Sequence service provider:</u> Roy J. Carver Biotechnology Center (Urbana, IL) at the University of Illinois<br><u>Sequencing method:</u> Illumina short read and 10x Genomics<br><u>Sequencing hardware:</u> Illumina short read and 10x Genomics

Publication:
The maize W22 genome provides a foundation for functional genomics and transposon biology.
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, Dawe RK, 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 2nd, 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, Brutnell TP.