@article {Jiao079004, author = {Yinping Jiao and Paul Peluso and Jinghua Shi and Tiffany Liang and Michelle C. Stitzer and Bo Wang and Michael S. Campbell and Joshua C. Stein and Xuehong Wei and Chen-Shan Chin and Katherine Guill and Michael Regulski and Sunita Kumari and Andrew Olson and Jonathan Gent and Kevin L. Schneider and Thomas K. Wolfgruber and Michael R. May and Nathan M. Springer and Eric Antoniou and Richard McCombie and Gernot G. Presting and Michael McMullen and Jeffrey Ross-Ibarra and R. Kelly Dawe and Alex Hastie and David R. Rank and Doreen Ware}, title = {Improved maize reference genome with single molecule technologies}, elocation-id = {079004}, year = {2017}, doi = {10.1101/079004}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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.}, URL = {https://www.biorxiv.org/content/early/2017/04/20/079004}, eprint = {https://www.biorxiv.org/content/early/2017/04/20/079004.full.pdf}, journal = {bioRxiv} }