RT Journal Article SR Electronic T1 The Sorghum bicolor reference genome: improved assembly and annotations, a transcriptome atlas, and signatures of genome organization JF bioRxiv FD Cold Spring Harbor Laboratory SP 110593 DO 10.1101/110593 A1 Ryan F. McCormick A1 Sandra K. Truong A1 Avinash Sreedasyam A1 Jerry Jenkins A1 Shengqiang Shu A1 David Sims A1 Megan Kennedy A1 Mojgan Amirebrahimi A1 Brock Weers A1 Brian McKinley A1 Ashley Mattison A1 Daryl Morishige A1 Jane Grimwood A1 Jeremy Schmutz A1 John Mullet YR 2017 UL http://biorxiv.org/content/early/2017/02/21/110593.abstract AB Sorghum bicolor is a drought tolerant C4 grass used for production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (~800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34,211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Sub-telomeric repeats with characteristics of Tandem Repeats In Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of the reference genome sequence to 56 resequenced genomes from diverse sorghum genotypes identified ~7.4M SNPs and 1.8M indels. Large scale variant features in euchromatin were identified with periodicities of ~25 kbp. An RNA transcriptome atlas of gene expression was constructed from 47 samples derived from growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement.