PT  - JOURNAL ARTICLE
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  - Kelly Dawe
AU  - Alex Hastie
AU  - David R. Rank
AU  - Doreen Ware
TI  - The complex sequence landscape of maize revealed by single molecule technologies
AID  - 10.1101/079004
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 079004
4099  - http://biorxiv.org/content/early/2016/12/19/079004.short
4100  - http://biorxiv.org/content/early/2016/12/19/079004.full
AB  - 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 crop, using Single Molecule Real-Time (SMRT) sequencing and high-resolution genome map. 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 region of low gene density region and maize lineage-specific genes.