next-generation sequencing, perennial plants, rhizomes, RNA-Seq, Sorghum halepense, transcriptomics, transcriptome analysis
Rhizomes facilitate the wintering and vegetative propagation of many perennial grasses. Sorghum halepense (johnsongrass) is an aggressive perennial grass that relies on a robust rhizome system to persist through winters and reproduce asexually from its rootstock nodes. This study aimed to sequence and assemble expressed transcripts within the johnsongrass rhizome. A de novo transcriptome assembly was generated from a single johnsongrass rhizome meristem tissue sample. A total of 141,176 probable protein-coding sequences from the assembly were identified and assigned gene ontology terms using Blast2GO. Estimated expression analysis and BLAST results were used to reduce the assembly to 64,447 high-confidence sequences. The johnsongrass assembly was compared to Sorghum bicolor, a related nonrhizomatous species, along with an assembly of similar rhizome tissue from the perennial grain crop Thinopyrum intermedium. The presence/absence analysis yielded a set of 98 expressed johnsongrass contigs that are likely associated with rhizome development.
Source Publication Title
American Society of Plant Biologists
Ryder, Nathan; Dorn, Kevin M.; Huitsing, Mark; Adams, Micah; Ploegstra, Jeff; DeHaan, Lee; Larson, Steve; and Tintle, Nathan L., "Transcriptome Assembly and Annotation of Johnsongrass (Sorghum Halepense) Rhizomes Identify Candidate Rhizome-Specific Genes" (2018). Faculty Work Comprehensive List. 960.