Metadata for assembly Zm-B73-REFERENCE-GRAMENE-4.0

Project: B73 Genome Assembly
BioProject: 
The reference genome of Zea mays sp. mays, inbred B73 was completely resequenced using PacBio Single Molecule Real-Time technology and a high-resolution genome map. Seed for the sequenced accession is available from NCRPIS (PI 677128).

BioSample: SAMN04296295

Assembly and sequencing:
<u>Assembly methods:</u> Celera Assembler PBcR–MHAP pipeline and Falcon. Quiver from SMRT Analysis v2.3.0 was used to polish base calling of contigs.<br><u>Construction of pseudomolecules:</u> Sequences from BACs used for v3 pseudomolecules were aligned to PacBio contigs using MUMMER. The scaffolds were then ordered and oriented into pseudochromosomes using the order of BACs as a guide. Gap filling was done with Pbjelly. The pseudomolecules were then polished using the Quiver pipeline from SMRT Analysis v2.3.0. Illumina 2500 Rapid was used to improve accuracy of base calls. These reads were aligned to the assembly using BWA-mem. SAMtools was used to generate the BAM format alignment for the Pilon pipeline.
<u>Sequence service provider:</u> Pacific Biosciences<br><u>Sequencing technologies:</u> PacBio SMRT<br><u>Sequencing method:</u> PacBio Single Molecule Real-Time sequencing

Publication:
Improved maize reference genome with single-molecule technologies
Yinping Jiao; Paul Peluso; Jinghua Shi; Tiffany Liang; Michelle C. Stitzer; Bo Wang; Michael Campbell; Joshua C. Stein; Xuehong Wei; Chen-Shan Chin; Katherine Guill; Michael Regulski; Sunita Kumari; Andrew Olson; Jonathan Gent; Kevin L. Schneider; Thomas K. Wolfgruber; Michael R. May; Nathan M. Springer; Eric Antoniou; Richard McCombie; Gernot G. Presting; Michael McMullen; Jeffrey Ross-Ibarra; Kelly Dawe; Alex Hastie; David R. Rank; Doreen Ware