TY - JOUR T1 - Improved maize reference genome with single molecule technologies JF - bioRxiv DO - 10.1101/079004 SP - 079004 AU - Yinping Jiao AU - Paul Peluso AU - Jinghua Shi AU - Tiffany Liang AU - Michelle C. Stitzer AU - Bo Wang AU - Michael S. Campbell AU - Joshua C. Stein AU - Xuehong Wei AU - Chen-Shan Chin AU - Katherine Guill AU - Michael Regulski AU - Sunita Kumari AU - Andrew Olson AU - Jonathan Gent AU - Kevin L. Schneider AU - Thomas K. Wolfgruber AU - Michael R. May AU - Nathan M. Springer AU - Eric Antoniou AU - Richard McCombie AU - Gernot G. Presting AU - Michael McMullen AU - Jeffrey Ross-Ibarra AU - R. Kelly Dawe AU - Alex Hastie AU - David R. Rank AU - Doreen Ware Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/04/20/079004.abstract N2 - Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate elucidation of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here, we report the assembly and annotation of maize, a genetic and agricultural model species, using Single Molecule Real-Time (SMRT) sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and significant improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed over 130,000 intact transposable elements (TEs), allowing us to identify TE lineage expansions unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by SMRT sequencing. In addition, comparative optical mapping of two other inbreds revealed a prevalence of deletions in the low gene density region and maize lineage-specific genes. ER -