De novo Assembly and Characterization of the Barnyardgrass (Echinochloa crus-galli) Transcriptome Using Next-Generation Pyrosequencing

BACKGROUND: Barnyardgrass (Echinochloa crus-galli) is an important weed that is a menace to rice cultivation and production. Rapid evolution of herbicide resistance in this weed makes it one of the most difficult to manage using herbicides. Since genome-wide sequence data for barnyardgrass is limited, we sequenced the transcriptomes of susceptible and resistant barnyardgrass biotypes using the 454 GS-FLX platform. RESULTS: 454 pyrosequencing generated 371,281 raw reads with an average length of 341.8 bp, which made a total length of 126.89 Mb (SRX160526). De novo assembly produced 10,142 contigs (∼5.92 Mb) with an average length of 583 bp and 68,940 singletons (∼22.13 Mb) with an average length of 321 bp. About 244,653 GO term assignments to the biological process, cellular component and molecular function categories were obtained. A total of 6,092 contigs and singletons with 2,515 enzyme commission numbers were assigned to 151 predicted KEGG metabolic pathways. Digital abundance analysis using Illumina sequencing identified 78,124 transcripts among susceptible, resistant, herbicide-treated susceptible and herbicide-treated resistant barnyardgrass biotypes. From these analyses, eight herbicide target-site gene groups and four non-target-site gene groups were identified in the resistant biotype. These could be potential candidate genes involved in the herbicide resistance of barnyardgrass and could be used for further functional genomics research. C(4) photosynthesis genes including RbcS, RbcL, NADP-me and MDH with complete CDS were identified using PCR and RACE technology. CONCLUSIONS: This is the first large-scale transcriptome sequencing of E. crus-galli performed using the 454 GS-FLX platform. Potential candidate genes involved in the evolution of herbicide resistance were identified from the assembled sequences. This transcriptome data may serve as a reference for further gene expression and functional genomics studies, and will facilitate the study of herbicide resistance at the molecular level in this species as well as other weeds.