The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization

Citation

Mccormick RF, Truong SK, Sreedasyam A, Jenkins J, Shu S, Sims D, Kennedy M, Amirebrahimi M, Weers BD, Mckinley B, Mattison A, Morishige DT, Grimwood J, Schmutz J, & Mullet JE (2017). The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. The Plant Journal 93:338–354.

Description

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.

Data Access

The sorghum reference genome sequence and annotation are available from Phytozome (phytozome.jgi.doe.gov). The sequence has also been deposited in GenBank under accession number ABXC00000000. The chloroplast sequence is available as GenBank Accession EF115542, and the mitochondrion sequence is available as NCBI Ref Seq accession NC_008360. Sequence reads for the 56 resequenced lines are available in the in the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) under the IDs provided in Data S5; the nine lines sequenced as part of this work are associated with BioProject PRJNA374837. RNA‐seq reads for the atlas are available from the NCBI SRA under accessions SRA558272, SRA558514 and SRA558539. Variant calls and RNA‐seq data are also hosted on the Phytozome JBrowse genome browser for browsing and download (phytozome.jgi.doe.gov).

Feedstocks
Biomass analytics
Genomics
RNA-seq