The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. (28th December 2017)

• Record Type: Journal Article
• Authors: McCormick, Ryan F.; Truong, Sandra K.; Sreedasyam, Avinash; Jenkins, Jerry; Shu, Shengqiang; Sims, David; Kennedy, Megan; Amirebrahimi, Mojgan; Weers, Brock D.; McKinley, Brian; Mattison, Ashley; Morishige, Daryl T.; Grimwood, Jane; Schmutz, Jeremy; Mullet, John E.
• Is Part Of: Plant journal. Volume 93:Number 2(2018)
• Page Start: 338
• Page End: 354
• Publication Date: 2017-12-28
• Subjects: discrete Fourier transform -- gene annotation -- genetic variation -- genome assembly -- kinase -- nucleosome occupancy -- reference genome -- satellite DNA -- Sorghum bicolor; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.13781
• Languages: English
• ISSNs: 0960-7412

Abstract

Summary: Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 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. Subtelomeric 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 more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4 M single nucleotide polymorphisms (SNPs) and 1.9 M indels. Large‐scale variant features in euchromatin were identified with periodicities of approximately 25 kbp. A transcriptome atlas of gene expression was constructed from 47 RNA‐seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and 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. Significance Statement: An improved reference genome assembly, genome annotation, and transcriptome atlas provide fundamental resources for basic and applied research in the agriculturally important plant Sorghum bicolor . These resources enabled the identification of subtelomeric tandem repeats specific to sorghum, revealed patterns of genetic variation accumulation in the genome, and identified a set of kinases putatively involved in regulating tissue identity.