Open AccessTranscriptome assembly and annotation of johnsongrass ( Sorghum halepense ) rhizomes identify candidate rhizome‐specific genes
Author(s) -
Ryder Nathan,
Dorn Kevin M.,
Huitsing Mark,
Adams Micah,
Ploegstra Jeff,
DeHaan Lee,
Larson Steve,
Tintle Nathan L.
Publication year - 2018
Publication title -
plant direct
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.211
H-Index - 11
ISSN - 2475-4455
DOI - 10.1002/pld3.65
Subject(s) - rhizome , biology , sorghum , perennial plant , contig , transcriptome , botany , gene , agronomy , genetics , gene expression , genome
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 Blast2 GO . 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.