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ARS Home » Pacific West Area » Logan, Utah » Forage and Range Research » Research » Publications at this Location » Publication #349205
Title: Transcriptome assembly and annotation of johnsongrass (Sorghum holepense) rhizomes identifies candidate rhizome-specific genes

Author
item RYDER, NATHAN - Dordt College
item DORN, KEVIN - Kansas State University
item HUITSING, MARK - Dordt College
item ADAMS, MICAH - Dordt College
item PLOEGSTRA, JEFF - Dordt College
item DEHAAN, LEE - The Land Institute
item Larson, Steven
item TINTLE, NATHAN - Dordt College

Submitted to: Plant Direct
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/23/2018
Publication Date: 5/23/2018
Citation: Ryder, N., Dorn, K.M., Huitsing, M., Adams, M., Ploegstra, J., Dehaan, L., Larson, S.R., Tintle, N.L. 2018. Transcriptome assembly and annotation of johnsongrass (Sorghum holepense) rhizomes identifies candidate rhizome-specific genes. Plant Direct. 2(6):e00065. https://doi.org/10.1002/pld3.65.
DOI: https://doi.org/10.1002/pld3.65

Interpretive Summary: Rhizomes are underground stems that facilitate the wintering and vegetative propagation of many different perennial grasses such as johnsongrass (Sorghum holepense) and intermediate wheatgrass (Thinopyrum intermedium). Johnsongrass and intermediate wheatgrass are very different warm-season and cool-season grasses, respectively. However, both species rely on underground rhizomes for winter survival and vegetative regrowth. Rhizomes are not present annual grasses and cereals, such as sorghum (Sorghum bicolor), even though some of these annuals are closely related to perennial grasses such as johnsongrass. The objective of this research was to sequence and compare expressed gene sequences from underground rhizomes and tillers of johnsongrass, intermediate wheatgrass, and one non-rhizomatous annual sorghum species (Sorghum bicolor) in search of genes that are conserved among different hizomatous perennial grasses. As part of this study, we sequenced and identified 141,176 protein-coding genes that were expressed in johnsongrass rhizomes. These new gene sequences were compared to other available gene sequences from underground tillers of non-rhizomatous annual sorghum grain crop species and underground rhizomes of intermediate wheatgrass. The presence/absence analysis yielded a set of 259 new gene sequences, from johnsongrass, that are evidently associated with rhizome development.

Technical Abstract: Rhizomes facilitate the wintering and vegetative propagation of many perennial grasses. Sorghum holepense (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. The johnsongrass assembly was compared to Sorghum bicolor, a related non-rhizomatous species, along with an assembly of similar rhizome tissue from the perennial grain crop Thinopyrum intermedium. The presence/absence analysis yielded a set of 259 johnsongrass contigs that are likely associated with rhizome development.