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. 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. C₄ photosynthesis genes including RbcS, RbcL, NADP-me and MDH with complete CDS were identified using PCR and RACE technology. 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.

Due to the diversity of Echinochloa species and the limited understanding of their damage processes in rice fields, clarifying the biological properties of distinct species could help create a foundation for effective control techniques. Pot experiments and field competition trials were conducted using eight Echinochloa species to elucidate their biological differences and assess their varying levels of negative impact on rice. The survey outcomes showed that E. oryzoides had the highest 1000-grain weight (3.12 g) while E. colona had the lowest (0.90 g). The largest grain number per spikelet found in E. glabrescens (940) was 3.4 times greater than that in E. oryzoides (277). Different species responded variably to changes in temperature and photoperiod. Except for E. caudate, all Echinochloa species exhibited a shortened growth period with the delay of the sowing date. Under field competitive conditions, all Echinochloa species exhibited significantly greater net photosynthetic rates than rice, with E. crusgalli exhibiting the highest photosynthetic capacity. Moreover, in this resource-limited setting, barnyardgrass species had a decrease in tiller formation and panicle initiation but a significant increase in plant height. These findings contribute valuable insights into the biological characteristics of barnyardgrass populations and provide guidance for implementing effective control measures in rice fields.

Barnyardgrass (Echinochloa crus-galli) is one of the most troublesome herbicide-resistant weeds worldwide that interferes with rice growth and rice yield. Here we provide the data from a comparative proteomic analysis of leaves in resistant (R) and susceptible (S) biotypes of Echinochloa crus-galli both with and without multi-herbicide treatment in two independent biological experiments using iTRAQ. The distribution of length and number of peptides, mass and sequence coverage of proteins were presented, and the repeatability of the replicates was analyzed. 1342 differential accumulated proteins were identified from 2248 unique peptides by searching uniprot database and data analysis. These results are associated with the research article "Quantitative proteomics reveals ecological fitness cost of multi-herbicide resistant barnyardgrass (Echinochloa crus-galli L.)" (X. Yang, Z. Zhang, T. Gu, M. Dong, Q. Peng, L. Bai, Y Li, 2017) [1].