RT Journal Article
SR Electronic
T1 The complex sequence landscape of maize revealed by single molecule technologies
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 079004
DO 10.1101/079004
A1 Yinping Jiao
A1 Paul Peluso
A1 Jinghua Shi
A1 Tiffany Liang
A1 Michelle C. Stitzer
A1 Bo Wang
A1 Michael S. Campbell
A1 Joshua C. Stein
A1 Xuehong Wei
A1 Chen-Shan Chin
A1 Katherine Guill
A1 Michael Regulski
A1 Sunita Kumari
A1 Andrew Olson
A1 Jonathan Gent
A1 Kevin L. Schneider
A1 Thomas K. Wolfgruber
A1 Michael R. May
A1 Nathan M. Springer
A1 Eric Antoniou
A1 Richard McCombie
A1 Gernot G. Presting
A1 Michael McMullen
A1 Jeffrey Ross-Ibarra
A1 Kelly Dawe
A1 Alex Hastie
A1 David R. Rank
A1 Doreen Ware
YR 2016
UL http://biorxiv.org/content/early/2016/12/19/079004.abstract
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.