Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
PLoS One. 2013 Jul 10;8(7):e69168. doi: 10.1371/journal.pone.0069168. Print 2013.
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.
稗草（Echinochloa crus-galli）是一种重要的杂草，对水稻种植和生产构成威胁。这种杂草对抗除草剂的快速进化使其成为最难用除草剂管理的杂草之一。由于稗草的全基因组序列数据有限，我们使用 454 GS-FLX 平台对敏感和抗除草剂稗草生物型进行了转录组测序。
454 焦磷酸测序生成了 371281 条原始reads，平均长度为 341.8bp，总长度为 126.89Mb（SRX160526）。从头组装产生了 10142 个 contigs（约 5.92Mb），平均长度为 583bp 和 68940 个 singletons（约 22.13Mb），平均长度为 321bp。大约 244653 个 GO 术语被分配到生物过程、细胞成分和分子功能类别。总共将 6092 个 contigs 和 singletons（具有 2515 个酶委员会编号）分配到 151 个预测的 KEGG 代谢途径。使用 Illumina 测序进行的数字丰度分析在敏感、抗除草剂处理的敏感和抗除草剂处理的抗性稗草生物型中鉴定了 78124 个转录本。从这些分析中，在抗性生物型中鉴定了八个除草剂靶标基因组和四个非靶标基因组。这些可能是稗草抗除草剂性中涉及的潜在候选基因，并可用于进一步的功能基因组学研究。使用 PCR 和 RACE 技术鉴定了包括 RbcS、RbcL、NADP-me 和 MDH 在内的 C4 光合作用基因，具有完整的 CDS。
这是首次使用 454 GS-FLX 平台对 E. crus-galli 进行大规模转录组测序。从组装序列中鉴定了参与除草剂抗性进化的潜在候选基因。该转录组数据可作为进一步基因表达和功能基因组学研究的参考，有助于在该物种以及其他杂草中研究除草剂抗性的分子水平。
